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70 results for “environmental dependence”
Density-dependent effects of exotic brook trout on aquatic communities in mountain lakes revealed by environmental DNA and morphological taxonomy
Invasion of non-native fishes threatens freshwater biodiversity worldwide. Yet, detailed estimates of population demography for invasive species, that estimate population size and body size of the invasive species, are rarely integrated in evaluating aquatic community responses. Our study capitalized on detailed brook trout population demographic data collected for a replicated whole lake ecosystem experiment involving experimental harvesting of exotic brook trout in nine mountain lakes. We applied environmental DNA (eDNA) metabarcoding and morphological taxonomy to examine the response of crustacean zooplankton and macroinvertebrate communities to gradients in brook trout effective density and lake elevation. Density-dependent effects of brook trout on crustacean zooplankton and macroinvertebrate communities were detected even decades after their first introductions (between 1926 and 1980). However, they were moderated by environmental factors such as elevation, lake maximum depth and dissolved organic carbon. Elevation was important in structuring crustacean zooplankton and macroinvertebrate community composition. While there were differences in explanatory variables when describing communities characterized by eDNA metabarcoding and morphological taxonomy, the principal environmental factors that structured the communities were similar. Our paper highlights persisting density-dependent impacts of exotic trout on invertebrate communities even decades after first introduction, and it considers the conservation implications for lake restoration.
The data behind the ApJ article "Environmental Dependence of Type Ia Supernovae in Low-Redshift Galaxy Clusters"
<p>Data from "Environmental Dependence of Type Ia Supernovae in Low-Redshift Galaxy Clusters", <a href="https://ui.adsabs.harvard.edu/abs/2023arXiv230601088L/abstract">NASA ADS</a></p><p>inner_cluster_data.csv and outer_cluster_data.csv include the SALT3 mB, x1, and c parameter values, distance moduli and Hubble residuals (with _1 referring to Figure 9 and _2 referring to Figure 10), outlier designation from MCMC procedure, host cluster, host cluster redshift (with Hubble diagram version converted to frame of CMB), host cluster r500, projected separation from cluster center, NED Host galaxy name, photometrically-derived estimate for host mass, host or SN redshift used in analysis, and the Host SFR category (Q: quiescent, SF: star-forming, GV: green valley) for our cluster SNe Ia.</p><p>sf_field.csv and quiescent_field.csv contain SALT parameter values, distance moduli and Hubble residuals (from Figure 10), host galaxy sSFR and mass measurements, and host redshifts (all spectroscopic, also with Hubble diagram converted values) for SNe Ia in our field samples.</p><p>full_cluster.csv contains the data from the table in the appendix of the paper.</p><p>The inner_cluster_/outer_cluster_mcmc_samples.csv files contain the samples needed to reproduce the corner plot for Figure 10.</p><p>The Python scripts recreate the figures from the paper given the above data. The details for which columns and constraints needed to reproduce the figures are included in these files.</p>
Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly
<p>Condition is assumed to reflect both genes and environment, enabling condition-dependent signals to reveal genetic quality. However, because the phenotypic effects of variation in genetic quality could be masked by environmental heterogeneity, the contribution of genetic quality to phenotypic variation in fitness-related traits and condition-dependent signals remains unclear. We compared effects of ecologically relevant manipulations of environmental quality (nutrient dilution in the larval diet) and genetic quality (one generation of inbreeding) on male and female morphology, life history and reproductive performance in the neriid fly <em>Telostylinus angusticollis</em>. We found that larval diet quality had strong, positive effects on male and female body size, male secondary sexual traits, and aspects of male and female reproductive performance. By contrast, inbreeding had weak effects on most traits, and no trait showed clear and consistent effects of both environmental and genetic quality. Indeed, inbreeding effects on body size and male competitive performance were of opposite sign in rich vs. poor larval diet treatment groups. Our results suggest that environmental quality strongly affects condition, but the effects of genetic quality are subtle and environment-dependent in this species. These findings raise questions about the genetic architecture of condition and the potential for condition-dependent traits to function as signals of genetic quality.</p>
Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
<p><strong><span>Aim</span></strong></p> <p><span>How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge for microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, its most influential drivers and their spatial scale dependence. </span></p> <p><strong><span>Location</span></strong></p> <p><span>Czech Republic.</span></p> <p><strong><span>Time period</span></strong></p> <p><span>Present.</span></p> <p><strong><span>Taxa studied</span></strong></p> <p><span>Fungi.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>We analyzed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition, climate) in fungi, using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.</span></p> <p><strong><span>Results</span></strong></p> <p><span>We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance-decay relationships</span><span>,</span><span> and their community composition was driven mainly by vegetation and dispersal at local scales, but at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.</span></p> <p><strong><span>Main conclusions</span></strong></p> <p><span>Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well-known patterns both from the macro- and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro- and macroorganisms. </span></p>
The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions
<p><span>Interspecific relationships between growth and survival are critical determinants of tree species diversity maintenance in forests. The trade-offs between growth and survival in co-occurring tree species are believed to arise along a continuum of life-history strategies. For example, co-occurring species range from those that grow slowly and survive well in resource-poor environments to those that grow quickly but have low survival rates in resource-rich environments. However, uncertainties remain regarding how growth-survival trade-offs are related to species traits, tree sizes, or environmental conditions.</span></p> <p><span>We examined how the relationships between species traits and growth–survival relationships shift in response to changes in stem sizes and across census periods with different climate conditions (frequency of strong winds, drought intensity) across 45 co-occurring tree species based on 23 years of growth and survival records in a warm temperate rain forest on Yakushima Island, Japan. We developed hierarchical Bayesian models of relative growth and survival rates, including leaf traits, wood density, and 95-percentile maximum stem diameter as explanatory variables. We tested the relationships between estimated trait-mediated growth–survival relationships and the intensities of climate events during five census periods.</span></p> <p><span>Each trait's effects on growth–survival relationships differed across the five census periods in response to climate conditions. Interspecific growth–survival relationships affected by a single trait axis for leaves or wood tended to be negative. In contrast, those affected by the maximum stem diameter tended to be positive. Such trends </span><span>increased with more frequent </span><span>strong winds or more intense droughts. The single-trait effects on growth–survival relationships were stronger for smaller sizes than for larger sizes. For all traits combined, we found a significant growth–survival trade-off only for small-sized stems in three of five census periods.</span></p> <p><span>Synthesis: Our results indicate that the effect of species traits on the growth–survival relationships depended on tree sizes, the census periods, or both in response to the frequency or intensity of climate events. We argue the importance of incorporating spatial and temporal variations in environmental conditions into long-term data from tree census to predict forest dynamics.</span></p>
The trait-mediated trade-off between growth and survival depends on tree sizes and environmental conditions
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Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly
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Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
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Data for Context-dependent biotic interactions control plant abundance across altitudinal environmental gradients, 2014, 2016, Colorado, USA
Many biotic interactions influence community structure, yet most distribution models for plants have focused on plant competition or used only abiotic variables to predict plant abundance. Furthermore, biotic interactions are commonly context-dependent across abiotic gradients. For example, plant-plant interactions can grade from competition to facilitation over temperature gradients. We used a hierarchical Bayesian framework to predict the abundances of 12 plant species across a mountain landscape and test hypotheses on the context-dependency of biotic interactions over abiotic gradients. We combined field-based estimates of six biotic interactions (foliar herbivory and pathogen damage, fungal root colonization, fossorial mammal disturbance, plant cover, and plant diversity) with abiotic data on climate and soil depth, nutrients, and moisture. All biotic interactions were significantly context-dependent along temperature gradients. Results supported the stress gradient hypothesis: As abiotic stress increased, the strength or direction of the relationship between biotic variables and plant abundance generally switched from negative (suggesting suppressed plant abundance) to positive (suggesting facilitation/mutualism). For half of the species, plant cover was the best predictor of abundance, suggesting that the prior focus on plant-plant interactions is well-justified. Explicitly incorporating the context-dependency of biotic interactions generated novel hypotheses about drivers of plant abundance across abiotic gradients and may improve the accuracy of niche models.
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>
Dependence of tropical cyclone weakening rate in response to an imposed moderate environmental vertical wind shear on the warm-core strength and height of the initial vortex
<p>This study investigated the dependence of the early tropical cyclone (TC) weakening rate in response to an imposed moderate environmental vertical wind shear (VWS) on the warm-core strength and height of the TC vortex using idealized numerical simulations. Results show that the weakening of the warm core by upper-level ventilation is the primary factor leading to the early TC weakening in response to an imposed environmental VWS. The upper-level ventilation is dominated by eddy radial advection of the warm-core air. The TC weakening rate is roughly proportional to the warm-core strength and height of the initial TC vortex. The boundary-layer ventilation shows no relationship with the early weakening rate of the TC in response to an imposed moderate VWS. The findings suggest that some previous diverse results regarding the TC weakening in environmental VWS could be partly due to the different warm-core strengths and heights of the initial TC vortex.</p>
Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies
<p>Examining how environmental factors influence phenotypic distribution might provide valuable information about local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of <em>Heliconius</em> butterflies displays a wide range of color patterns across the Neotropics and is involved in several hybrid zones, making it an excellent system to study color phenotypic distribution. Using a multiscale distribution strategy, we studied whether different phenotypes of the distantly related species <em>H. erato</em> and <em>H. melpomene,</em> belonging to the red-yellow mimetic ring, are associated with different environmental conditions. We show that environmental gradients (particularly heat and precipitation factors) drive <em>Heliconius</em> phenotypic distributions, but that phenotype and environmental correlations vary with spatial scale. While co-mimics are frequently found in similar environments at a broad scale, patterns at the local level are not necessarily consistent (different variables are the best predictors of phenotypic occurrence in different areas) or congruent (co-mimic pairs show distinct associations with the environment). Thus, large-scale analysis may help to identify how environmental heterogeneity influences broad mimic phenotypic distributions, but local studies are needed to understand the context-dependent biotic, abiotic, and historical mechanisms that drive finer-scale phenotypic shifts.</p>
Data from: Stressful city sounds: glucocorticoid responses to experimental traffic noise are environmentally dependent
A major challenge in urban ecology is to identify the environmental factors responsible for phenotypic differences between urban and rural individuals. However, the intercorrelation between the factors that characterise urban environments, combined with a lack of experimental manipulations of these factors in both urban and rural areas, hinder efforts to identify which aspects of urban environments are responsible for phenotypic differences. Among the factors modified by urbanisation, anthropogenic sound, particularly traffic noise, is especially detrimental to animals. The mechanisms by which anthropogenic sound affects animals are unclear, but one potential mechanism is through changes in glucocorticoid hormone levels. We exposed adult house wrens, Troglodytes aedon, to either traffic noise or pink noise. We found that urban wrens had higher initial (pre-restraint) corticosterone than rural wrens before treatment, and that traffic noise elevated initial corticosterone of rural, but not urban, wrens. By contrast, restraint stress-induced corticosterone was not affected by noise treatment. Our results indicate that traffic noise specifically contributes to determining the glucocorticoid phenotype, and suggest that glucocorticoids are a mechanism by which anthropogenic sound causes phenotypic differences between urban and rural animals.
Data for effects of multiple drivers of environmental change on native and invasive macroalgae in nearshore groundwater dependent ecosystems
<p><strong><em>Okuhata, B.K., Delevaux, J.M.S., Richards Donà, A., Smith, C.M., Gibson, V.L., Dulai, H., El-Kadi, A.I., Stamoulis, K., Burnett, K.M., Wada, C.A., Bremer, L.L., Effects of multiple drivers of environmental change on native and invasive macroalgae in nearshore groundwater dependent ecosystems</em></strong></p> <p>Environmental change scenarios, with a spatial extent of the Keauhou basal aquifer (Hawai‘i), were produced using a recharge coverage from Engott (2011), land use coverages from the State of Hawai‘i (2022) and National Oceanic and Atmospheric Administration (2006); climate change calculations based on Elison Timm et al. (2015), and native forest conversion calculations from Bremer et al. (2021). Scenarios were developed based on the following assumptions:</p> <p>Scenario 0 (Baseline) assumes current land use, groundwater recharge, and groundwater withdrawal rates (National Oceanic and Atmospheric Administration, 2006; State of Hawai‘i, 2022; Engott, 2011; Commission on Water Resource Management, unpublished data, 2018). Please see Okuhata et al. (2021) for more details regarding the scenario assumptions for the baseline groundwater model.</p> <p>Scenario 1 (Climate Change) assumes current land use, but with Representative Concentration Pathway (RCP) 8.5 mid-century rainfall projections (Elison Timm et al., 2015), where rainfall and recharge calculations were based on estimates from Giambelluca et al. (2013) and Engott (2011). </p> <p>Scenario 2 (Urban Development) assumes RCP 8.5 mid-century rainfall conditions along with future permitted development, which includes an increase in water demand (Fukunaga & Associates, Inc., 2017). </p> <p>Scenario 3 (Native Forest Conversion + Urban Development) assumes RCP 8.5 mid-century rainfall conditions and future permitted development, along with the assumption that native forests are not protected and converted to non-native forests (Bremer et al., 2021), therefore altering recharge estimates (Wada et al., 2017; Engott, 2011).</p> <p>Please note that scenario numbers listed in the groundwater model and marine water quality model shapefiles may differ from the manuscript scenario numbers. The following table assigns the scenario numbers to their respective scenarios in the manuscript, groundwater model, and marine water quality model.</p> <table> <tbody> <tr> <td> <p><strong>Scenario Name</strong></p> </td> <td> <p><strong>Manuscript #</strong></p> </td> <td> <p><strong>Groundwater Model #</strong></p> </td> <td> <p><strong>Marine Water Quality Model #</strong></p> </td> </tr> <tr> <td> <p>Baseline</p> </td> <td> <p>Scenario 0</p> </td> <td> <p>Scenario 1</p> </td> <td> <p>Scenario 0</p> </td> </tr> <tr> <td> <p>Climate Change</p> </td> <td> <p>Scenario 1</p> </td> <td> <p>Scenario 2</p> </td> <td> <p>Scenario 1</p> </td> </tr> <tr> <td> <p>Urban Development</p> </td> <td> <p>Scenario 2</p> </td> <td> <p>Scenario 7</p> </td> <td> <p>Scenario 6</p> </td> </tr> <tr> <td> <p>Native Forest Conversion + Urban Development</p> </td> <td> <p>Scenario 3</p> </td> <td> <p>Scenario 5</p> </td> <td> <p>Scenario 4</p> </td> </tr> </tbody> </table> <p>The groundwater model results are in shapefile format and were produced using the program SEAWAT (Langevin et al., 2008). The spatial extent is the Keauhou basal aquifer, and the projection is NAD 1983 UTM Zone 4N. The two polygon shapefiles represent the first and second layers of the groundwater model, and include groundwater level (meters relative to mean sea level), salinity (parts per thousand), temperature (degrees Celsius), nitrogen (milligrams per liter), and phosphorus (milligrams per liter) results under the assumptions of each scenario. The point shapefile represents the simulated discharge at SGD plumes under the assumptions of each scenario.</p> <p>The marine water quality model results are in floating point TIFF format and were produced using the program R software. The spatial extent is the coastal area of the Keauhou aquifer system, and the geographic coordinate system is WGS 1984. The files include the groundwater discharge (cubic meters per month), salinity (parts per thousand), temperature (degrees Celsius), nitrogen (kilograms per month), and phosphorus (kilograms per month) results under the assumptions of each scenario.</p> <p>The limu model results are in shapefile format and were produced using the program R software. The spatial extent is the coastal area of the Keauhou aquifer system, and the geographic coordinate system is WGS 1984. The files include the increase and decrease in area (hectares) for <em>Ulva lactuca</em> and <em>Hypnea musciformis </em>under the assumptions of each scenario.</p> <p>The limu experiment results are derived from a csv file, which reports the <em>Ulva lactuca</em> and <em>Hypnea musciformis </em>measured weights (initial and final) for each growth run. These were used to calculate the weight difference. Included also in the dataset are the fixed and random effects used in the R script to run the model.</p> <p>Contact Leah Bremer (<a href="mailto:lbremer@hawaii.edu">lbremer@hawaii.edu</a>) or Brytne Okuhata (bokuhata@hawaii.edu) of the University of Hawaiʻi for more information on these files.</p>
Data from: Trait interactions effects on tropical tree demography depend on the environmental context
<p><span class="fontstyle0">Although functional traits are defined based on their impact on demographic parameters, trait-demography relationships are often reported as weak. These weak relationships might be due to disregarding trait interactions and environmental contexts, which should modulate species trait-demography relationships. We applied different models, including boosted regression tree (BRT) models, to investigate changes in the relationship between traits and demographic rates of tropical tree species in plots along an elevational gradient and among time intervals between censuses, analyzing the effect of a strong drought event. Based on a large dataset of 18,000 tree individuals from 133 common species, distributed among twelve 1-ha plots (habitats) in the Atlantic Forest (Brazil), we evaluated how trait interactions and the environmental context influence the demographic rates (growth, mortality, and recruitment). Functional traits, trait-trait, and trait-habitat interactions predicted demography with a good fit through either BRTs or linear mixed-models. Changes in growth rates were best related to size (diameter), and mortality rates to habitats, while changes in recruitment rates were best related to the specific leaf area. Moreover, the influence of traits differed among time intervals, and for demographic parameters, habitat affected growth and mortality by interacting with diameter. Here, we provide evidence that trait-demography relationships can be improved when considering the environmental context (space and time) and trait interactions to cope with the complexity of changes in the demography of tropical tree communities. Thus, to expand predictions of demography based on functional traits, we show that it is useful to fully incorporate the concept of multiple trait-fitness optima, resulting from trait interactions in different habitats and growth conditions.</span> </p>
The effects of sex on extinction dynamics of Chlamydomonas reinhardtii depend on the rate of environmental change
<p>The continued existence of sex, despite many the costs it entails, still lacks an adequate explanation, as previous studies demonstrated that the effects of sex are environment-dependent: sex enhances the rate of adaptation in changing environments, but the benefits level off in benign conditions. To the best of our knowledge, the potential impact of different patterns of environmental change on the magnitude of these benefits received less attention in theoretical studies. In this paper, we begin to explore this issue by examining the effect of the rate of environmental deterioration (negatively correlated with population survival rate), on the benefits of sex.</p> <p>To investigate the interplay of sex and the rate of environmental deterioration, we carried out a long-term selection experiment with a unicellular alga (<em>Chlamydomonas</em> <em>reinhardtii</em>), by manipulating mode of reproduction (asexual, facultative or obligate sexual) and the rate of environmental deterioration (an increase of salt concentration). We monitored both the population size and extinction dynamics.</p> <p>The results revealed that the relative advantage of sex increased at the intermediate rate and plateaued at the highest rate of environmental deterioration. Obligate sexual populations had the slowest extinction rate under the intermediate rate of environmental deterioration, while facultative sexuality was favoured under the high rate-treatment.</p> <p>To the best of our knowledge, our study is the first to demonstrate that the interplay of sex and the rate of environmental deterioration affects the probability of survival, which indicates that mode of reproduction may be an important determinant of survival of the anthropogenic-induced environmental change.</p>
Data from: The quantity of deposited environmental DNA in plant-insect interactions depends on taxon, abundance, and interaction time
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Species traits mediate environmental responses but not conspecific density dependence in tropical tree saplings
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Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies
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Data from: Scale-dependent responses to environmental fluctuations in tropical tree species’ crown temperatures
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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)
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DANDI Archive for NWB datasets
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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.