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151 results for “Ecological scales”
Data supplementing the article "Assessing ecological status with diatoms DNA metabarcoding : scaling-up on a WFD monitoring network (Mayotte island, France)" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal
<p>These data supplement the article"Assessing ecological status with DNA metabarcoding or microscopy? Comparison using benthic diatoms in tropical rivers" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal.</p> <p>The directory contains the following files:</p> <p><strong>80 PGM sequencing libraries (raw data, fastq files).rar </strong>- contains the 80 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>80 fastq files information.xlsx</strong> - contains the information relative to the 80 samples including: the ID used in Mothur analyses (corresponding to the name of the fastq files), the sample name, the sampling site code, the name of the river, the monitoring network to which rivers belong, the year of sampling and the GPS coordinates of sampling sites.</p> <p><strong>OTU (95 percent of similarity) list of 80 Mayotte samples.xlsx</strong> - contains the final OTU list obtained after applying all the bioinformatics treatments (trimming, clustering,...): OTUs created at 95% of similarity, the number of DNA reads per sample was normalized at 5710 reads (the smallest values obtained in one sample). A DNA representative sequence and the taxonomic assignment determined using Mothur (using classify.otu command) are also provided for each OTU.</p>
Urban Stream Environmental and Sequencing Datasets for Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams
<p>The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper <strong>Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams </strong>submitted to Applied and Environmental Microbiology. </p>
A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
<p>Tropical ecosystems are often biodiversity hotspots, and invertebrates represent the main underrepresented component of diversity in large-scale analyses. This problem is partly related to the scarcity of data widely available to conduct these studies and the lack of systematic organization of knowledge about invertebrates' distributions in biodiversity hotspots. Here, we introduce and analyze a comprehensive data compilation of Amazonian ant diversity. Using records from 1817 to 2020 from both published and unpublished sources, we describe the diversity and distribution of ant species in the Brazilian Amazon Basin. Further, using high-definition images and data from taxonomic publications, we build a comprehensive database of morphological traits for the ant species that occur in the region. In total, we recorded 1,067 nominal species in the Brazilian Amazon Basin, with sampling locations strongly biased by access routes, urban centers, research institutions, and major infrastructure projects. Large areas where ant sampling is non-existent represent about 52% of the basin and are concentrated mainly in the North, Southeastern, and Western Brazilian Amazon. We found that distance to roads is the main driver of ant sampling in the Amazon. Contrary to our expectations, morphological traits had lower predictive power in predicting sample bias than purely geographic variables. However, when geographic predictors were controlled, habitat stratum and traits contribute to explain the remaining variance. More species were recorded in better-sampled areas, but species richness estimation models suggest that areas in South Amazonian edge forests are associated with especially high species richness. Our results represent the first trait-based, large-scale study for insects in Amazonian forests and a starting point for macroecological studies focusing on insect diversity in the Amazon Basin.</p>
Data for "Testing for variation in photoperiodic plasticity in a butterfly: inconsistent effects of circadian genes between geographic scales" (Ecology and Evolution, accepted manuscript)
<p>Raw data and analysis scripts belonging to <em>Testing for variation in photoperiodic plasticity in a butterfly: inconsistent effects of circadian genes between geographic scales</em> (Ecology and Evolution, accepted manuscript).</p> <p>Includes data from a photoperiodic assay with larvae of the speckled wood butterfly, <em>Pararge aegeria</em>, as well as a small bioinformatic analysis of SNP variation in two circadian candidate genes.</p> <p>List of files:</p> <table> <tbody> <tr> <td>statistics_and_figures.R</td> <td>Statistical analysis of phenotyping experiment; drawing figures</td> </tr> <tr> <td>variant_calling.sh</td> <td>Shell script for mapping sequencing reads; calling and tabulating SNPs</td> </tr> <tr> <td>experiment_diapause.txt</td> <td>Data from phenotyping experiment, for analysis of diapause induction</td> </tr> <tr> <td>experiment_larval</td> <td>Data from phenotyping experiment, for analysis of larval development</td> </tr> <tr> <td>snptable_timeless</td> <td>Tabulated allele frequencies for exonic SNPs in timeless</td> </tr> <tr> <td>snptable_period</td> <td>Tabulated allele frequencies for exonic SNPs in period</td> </tr> </tbody> </table>
Data and code for the manuscript: "An ecological explanation for hyperallometric scaling of reproduction"
<p>Code, data, and data objects underlying the analyses presented in the manuscript "An ecological explanation for hyperallometric scaling of reproduction".</p> <p>A version of the manuscript is available on bioRxiv: https://doi.org/10.1101/2021.03.12.435090</p> <p>Abstract for the manuscript:</p> <p>"In wild populations, large individuals have disproportionately higher reproductive output than smaller individuals. Some theoretical models explain this pattern – termed reproductive hyperallometry – by individuals allocating a greater fraction of available energy towards reproductive effort as they grow. Here, we propose an ecological explanation for this observation: differences between individuals in rates of resource assimilation, where greater assimilation causes both increased reproduction and body size, resulting in reproductive hyperallometry at the level of the population. We illustrate this effect by determining the relationship between size and reproduction in wild and lab-reared Trinidadian guppies. We show that (i) reproduction increased disproportionately with body size in the wild but not in the lab, where resource competition was eliminated; (ii) in the wild, hyperallometry was greatest during the wet season, when resource competition is strongest; and (iii) detection of hyperallometric scaling of reproduction at the population level was inevitable if individual differences in assimilation were ignored. We propose that ecologically-driven variation in assimilation – caused by size-dependent resource competition, niche expansion, and chance – contributes substantially to hyperallometric scaling of reproduction in natural populations. We recommend that mechanistic models incorporate such ecologically-caused variation when seeking to explain reproductive hyperallometry.'</p> <p>The zip file contains:</p> <p>1. A single R script for running the analyses, generating the results, and producing the figures given in the manuscript </p> <p>- size_reproduction_scaling_lab_wild.R </p> <p>2. Two .csv files containing the wild and lab datasets used in the study:</p> <p>- wild_guppy_data_81-87.csv (the wild dataset)<br> - senecence_long_data.csv (the lab dataset)</p> <p>3. A folder containing 14 model objects. These are the models produced by running the R script. These are provided to save the user time. The model object names correspond to the models described in Table 1 of the manuscript.</p> <p>4. A READ_ME.txt file.</p>
Data and codes to replicate the analysis in: The spatial ecology of conflicts: Unravelling patterns of wildlife damage at multiple scales
<p><span><span>Human encroachment into natural habitats is typically followed by conflicts derived from wildlife damages to agriculture and livestock. Spatial risk modelling is a useful tool to gain understanding of wildlife damage and mitigate conflicts. Although resource selection is a hierarchical process operating at multiple scales, risk models usually fail to address more than one scale, which can result in the misidentification of the underlying processes. Here, we addressed the multi-scale nature of wildlife damage occurrence by considering ecological and management correlates interacting from household to landscape scales. We studied brown bear (<i>Ursus arctos</i>) damage to apiaries in the North-eastern Carpathians as our model system. Using generalized additive models, we found that brown bear tendency to avoid humans and the habitat preferences of bears and beekeepers determine the risk of bear damage at multiple scales. Damage risk at fine scales increased when the broad landscape context also favoured damages. Furthermore, integrated-scale risk maps resulted in more accurate predictions than single-scale models. Our results suggest that principles of resource selection by animals can be used to understand the occurrence of damages and help mitigate conflicts in a proactive and preventive manner. </span></span></p>
Vegetation cover and biodiversity reduce parasite infection in wild hosts across ecological levels and scales
<p><span>Land use changes and biodiversity loss critically disrupt ecosystem functioning and are major drivers of infectious disease outbreaks. <em>Trypanosoma</em> <em>cruzi</em>, the agent of Chagas disease, is a multi-host parasite whose epidemiology has changed due to the expansion of anthropogenic activities over natural areas. We aimed to understand the ecological processes increasing parasite prevalence at the individual, the community and the landscape levels using the largest database on small mammal infection by <em>T. cruzi</em> in Brazil. We applied machine learning techniques and structural equation models to show that allometric traits and the relative abundance of rodents in the community were important predictors of infection risk, followed by variables associated with the landscape environmental </span><span>quality</span><span>. Natural vegetation cover change and the taxonomic and functional dimensions of biodiversity indirectly reduced infection through its effect on the abundance distribution and composition of host communities. According to our findings, approaches to biodiversity conservation and restoration based on the integration of social inclusion and human welfare would contribute to regulating the prevalence of <em>T. cruzi</em> in wild hosts, which may reduce overall transmission risk.</span></p>
Interview Transcriptions related to PhD Thesis "Degrowth at a Global Scale? Geographies of Chile's Fruit Production and Export between Extractivism and Socio-Ecological Transformation"
<p>The material is composed of transcriptions of interviews conducted for the empirical work of this PhD Thesis.</p> <p>Not all conducted interviews are included (which can be seen from the accompanying table); those not included are not available mostly due to lack of consent of interviewees or because certain interviews were not registered and only hand-written notes were taken.</p>
Fig. 3. Isolated type A coprolites viewed using transmitted-light microscopy. Scale bars 100 in The ecological role of immature phantom midges (Diptera: Chaoboridae) in the Eocene Lake Messel, Germany
Fig. 3. Isolated type A coprolites viewed using transmitted-light microscopy. Scale bars 100 µm.
Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient
<p>Title of dataset</p> <p>Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient</p> <p>Authors of dataset</p> <p>Leon Marshall<sup>1,2</sup>, John S. Ascher<sup>3</sup>, Cristian Villagra<sup>4</sup>, Amaury Beaugendre<sup>1</sup>, Valentina Herrera<sup>4</sup>, Patricia Henríquez-Piskulich<sup>4</sup>, Alejandro Vera<sup>5</sup>, Nicolas J. Vereecken<sup>1</sup></p> <ol> <li>Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/2, B 1050 Brussels, Belgium</li> <li>Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands</li> <li>Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore</li> <li>Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> <li>Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> </ol> <p>Abstract</p> <p>Chile's isolation and varied climates have driven the evolution of a unique biodiversity with a high degree of endemism. As a result, Chile encompasses diverse environments, including the Mediterranean-type ecosystem, a global biodiversity hotspot. These environments are currently threatened by anthropogenic land use change impacting the integrity of local biomes and associated species. This area is the most intensively sampled of the country with high endemicity of native bee species. Characterising habitat requirements of bees is a pressing priority to safeguard these insects and the ecosystem services they provide. We investigated broad-scale patterns of bee (Hymenoptera: Apoidea: Anthophila) diversity using newly accessible expert-validated datasets comprising digitized specimen records from Chilean and US collections, and novel expert-validated type specimen data for the bees of Chile. We used a generalised dissimilarity modelling (GDM) approach to explore both compositional and phylogenetic β-diversity patterns across latitudinal, altitudinal, climate and habitat gradients in well-sampled bee assemblages in Central Chile. Using the GDM measures of increasing compositional and environmental dissimilarity we categorised and compared the most important drivers of these patterns and used them to classify 'wild bee ecoregions' (WBE) representing unique assemblages. Turnover of bee assemblages was explained primarily by latitudinal variation (proxy for climate) from south to north in Chile. However, temperature variations, precipitation and the presence of bare soil also significantly explained turnover in bee assemblages. In comparison, we observed less turnover in phylogenetic biodiversity corresponding to spatial gradients. We identified six de novo ecoregions (WBE), all with distinct taxa, endemic lineages, and representative species. The WBE represent distinct spatial classifications but have similarities to existing biogeographical classifications, ecosystems and bioclimatic zones. This approach establishes the baseline needed to prioritise bee species conservation efforts across this global biodiversity hotspot. We discuss the novelty of this classification considering previous biogeographical characterisations and their relevance in assessing conservation priorities for bee conservation. We argue that Chile's WBE highlight areas in need of funding for bee species surveys and description, distribution mapping and strengthening of conservation policies.</p> <p>Usage notes</p> <p>The dataset contains species occurrence data of chilean bees aggregated to a 5 x 5 km grid shapefile. The shapefile of the grid and the raster mask of the Central Chilean study area are also included. Finally, a database of type specimen data used to supplement the dataset is included here. The code for the analysis can be found at: <a href="https://github.com/lmar116/ChileanBeeDiversity">https://github.com/lmar116/ChileanBeeDiversity</a>.</p> <p>Shapefiles, rasters, CSV files and code were all loaded and analyzed using R statistics software. </p> <p>Four files are included:</p> <ol> <li>Marshall-et-al-2023_Ecosphere_DataTable_bee_grid: contains all species occurrence data used in GDM analysis, Grid column refers to cl.5km.shp.</li> <li>cl.5km.shp (and associated files): 5 x 5 km grid shapefile of the Central Chilean study area</li> <li>chile.mask.tif: raster outline of the Central Chilean study area</li> <li>Marshall-et-al-2023_Ecosphere_CentralChileTypeSpecimens.xlsx: contains type specimen data used to supplement species occurrence dataset.</li> </ol>
Fine-scale intraspecific niche partitioning in a highly mobile, marine megafauna species: implications for ecology and conservation
<p>A species may partition its realized ecological niche along bionomic and/or scenopoetic axes due to intraspecific competition for limited resources. How partitioning manifests depends on resource needs and availability by and for the partitioning groups. Here we demonstrate the utility of analyzing short- and long-term stable carbon and nitrogen isotope ratios from imperiled marine megafauna to elucidate realized niche partitioning in these species. We captured 113 loggerhead (<em>Caretta</em> <em>caretta</em>) sea turtles at a high-use area near Crystal River, Florida, between 2016–2022, comprising 53 subadults, 10 adult males, and 50 adult females. Isotopic analyses indicated that loggerheads partition their realized ecological niche by life stage, along a scenopoetic axis. Most adults likely forage and reside in shallow areas of the study site, with most subadults displaying habitat switching between deeper locations to forage and shallower locations to rest. Some subadults, like adults, also forage and reside in shallow areas, and may display behaviors to avoid intraspecific competition. Analysis of stable isotopes with different turnover rates was critical for this characterization of intraspecific niche partitioning in loggerhead turtles, which has direct implications for ongoing research and conservation efforts for this and other imperiled species.</p>
Scale-dependence of ecological assembly rules: insights from empirical datasets and joint species distribution modelling
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Habitat-scale ecological data for the <em>Adiantum pedatum</em> complex in northeastern North America
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Data from: Ecological differentiation facilitates fine-scale coexistence of sexual and asexual Boechera
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Data from: Warm acclimation reduces the sensitivity of Drosophila species to heat stress at ecologically relevant scales
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Fine-scale intraspecific niche partitioning in a highly mobile, marine megafauna species: implications for ecology and conservation
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Behaviour across time and space–how large scale ‘trait-based’ approaches can shape behavioural ecology
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Data from: Boreal tree growth exhibits decadal-scale ecological memory to drought and insect defoliation, but no negative response to their interaction
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A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
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Large-scale patterns of green turtle trophic ecology in the eastern Pacific Ocean
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International Brain Laboratory public data
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OpenNeuro
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