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2,603 results for “Ecological data”
Interagency Ecological Program: Discrete water quality and phytoplankton data from the Sacramento River floodplain and Yolo Bypass tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998 - 2022
The Yolo Bypass Fish Monitoring Program (YBFMP) operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Program objectives include: Collecting baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance; Analyzing and communicating Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management related questions; Providing technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. We collect discrete water quality data using a YSI ProDSS and sample phytoplankton, chlorophyll and nutrients as discrete water grabs taken biweekly (or weekly during Yolo Bypass inundation) along with lower trophic tows. Water is sampled at three sites along the Yolo Bypass and Sacramento River, then processed and analyzed by an internal DWR laboratory.
Interagency Ecological Program: Data for Synthesis for Ecological Impacts of Drought in the Upper San Francisco Estuary, 1975-2021
These data were collected for the special issue on Drought in the Sacramento-San Joaquin Delta published in San Francisco Estuary and Watershed Sciences, Volume 22, Issue 1, March of 2024. Multi-year droughts are important and impactful features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem response of the San Francisco Estuary and the Sacramento-San Joaquin Delta. This data set was assembled from data collected by long-term monitoring programs over the past 46 years (1975-2021) to evaluate how the estuary changed during multi-year droughts. Data include fish, zooplankton, jellyfish, clams, temperature, Secchi depth, and salinity as measured by fish and water quality surveys, as well as nutrients and chlorophyll measured by water quality surveys. These data are accompanied by hydrologic metrics including Delta Inflow, Delta Outflow, the position of the 2-PSU isohaline, residence time, and daily values of various continuous water quality stations located in the Delta.
Interagency Ecological Program and US Fish and Wildlife Service: Enhanced Delta Smelt Monitoring Program Experimental Larval Survey Data 2018-2019
The United States Fish and Wildlife Service’s (USFWS) Experimental Larval Survey was designed and implemented by the Enhanced Delta Smelt Monitoring Program to assess alternative sampling methods for monitoring the larval life stages of the federally endangered Delta Smelt (Hypomesus transpacificus) within the San Francisco Estuary, California, USA. From 2018 to 2019, four different sampling methods (Beach Seine, Manta Trawl Net, 20-mm Surface Trawl Net, 20-mm Midwater Trawl Net) nested in time and space were used to estimate the occupancy rate, relative density, and size distribution of larval Delta Smelt across sampling methods and water depth strata within the San Francisco Estuary. For more information on the Lodi USFWS Office and the Enhanced Delta Smelt Monitoring Program: https://www.fws.gov/lodi/.
Throw trap and electrofishing data collected during 1996–2022 from the Everglades, Florida, United States for the publication "Hydrology-mediated ecological function of a large wetland threatened by an invasive predator"
Asian swamp eels (Monopterus albus/javanensis complex) were first reported from Florida in 1997 and the Everglades in 2007; swamp eels have been established in Taylor Slough of Everglades National Park since 2014. This dataset incorporates plot-level mean densities (# of individuals per square meter) of common aquatic animals collected during 1996–2022 from 24 sites across four regions of the Everglades: Taylor Slough, Shark River Slough, Water Conservation Area 3, and the C-111 Panhandle. Prey species included are the six most common small fishes prior to swamp eel invasion of Taylor Slough (1996–2009) and the three common decapod species (two crayfish species and grass shrimp). An annual index of mean wet season electrofishing catch-per-unit-effort of swamp eels, Mayan cichlids (Mayaheros uruphthalmus), and the three other large 'top predator' fishes (Amia calva, Lepisosteus platyrhincus, Micropterus salmoides) is included for plots where electrofishing was performed from 1997-2021. Hydrologic measures used in analyses are included.
Mark-recapture data of the northern spring salamander (Gyrinophilus porphyriticus) in support of 2023 Lowe et al. Ecology
This dataset includes spatially explicit mark-recapture data of the Northern Spring Salamander (Gyrinophilus porphyriticus) collected during the summer months (June – August) from downstream and upstream reaches in multiple streams in the Hubbard Brook Experimental Forest. Downstream reaches begin at the confluence with the Main Hubbard and extend upstream 500 meters and upstream reaches begin at the weir and extend downstream 500 meters. Downstream reaches contain brook trout and upstream reaches do not. We used a robust design framework with 9 surveys per reach each summer (3 primary occasions with 3 secondary occasions each). Salamanders were captured by hand and marked with either Visual Implant Elastomer and/or a PIT tag. The data table herein is specific to the following publication: Lowe, W.H., B.R. Addis, M.M. Cochrane, and L.K. Swartz. In press. Source-sink dynamics within a complex life history. Ecology. These data are a subset of the primary long term dataset available at https://doi.org/10.6073/pasta/cd5f5a03df194930bf87eb12157b8182 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Data and code from "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" Kaiser et al. 2023 Behavioral Ecology and Sociobiology
This dataset is published in support of "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" by Kaiser et al. 2023 in Behavioral Ecology and Sociobiology. Data and code to test the assumptions and key predictions of the Trivers-Willard hypothesis, which proposes that females produce more sons or daughters depending on food availability, in the black-throated blue warbler at the Hubbard Brook Experimental Forest, NH, 2007-2012. Datasets support analyses of sex ratio bias at both the nest and nestling levels. Data tables support the comparison of the ratio of variances in the scaled pre-fledging mass of male and female nestlings using an F test and reproduction of Figures 2a and 2b. Figures are those used in the published manuscript. Code supports the calculation of offspring sex ratio bias at the population level, and considering separately both low- and high-quality habitats, using the Neuhäuser test, statistical models testing the assumptions of the Trivers-Willard hypothesis, effects of food availability and parental provisioning on offspring sex ratio, and effects of food availability on pre-fledging nestling mass of sons and daughters, and a power analysis to determine the power to detect an effect of food supplementation on sex ratio. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the US Forest Service, Northern Research Station.
Data and code from "Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability" Kaiser et al. 2024 Ecology and Evolution
Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing ‘green’ season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a two-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons. These data were gathered as part of the Hubbard Brook Ecosystem Study (HB
MCR LTER: Coral Reef: Priority effects in coral-macroalgae interactions can drive alternate community paths in the absence of top-down control, data for Adam 2022 Ecology
These data were generated in support of the manuscript: Adam TC, Holbrook SJ, Burkepile DE, Speare KE, Brooks AJ, Ladd MC, Shantz AA, Thurber RLV, and Schmitt RJ, Ecology The outcomes of species interactions can vary greatly in time and space with the outcomes of some interactions determined by priority effects. On coral reefs, benthic algae rapidly colonize the disturbed substrate. In the absence of top-down control from herbivorous fishes, these algae can inhibit the recruitment of reef-building corals, leading to a persistent phase shift to a macroalgae-dominated state. Yet, corals may also inhibit colonization by macroalgae, and thus the effects of herbivores on algal communities may be strongest following disturbances that reduce coral cover. Here, we report results from experiments conducted on the fore reef of Moorea, French Polynesia, where we: 1) tested the ability of macroalgae to invade coral-dominated and coral-depauperate communities under different levels of herbivory, 2) explored the ability of juvenile corals (Pocillopora spp.) to suppress macroalgae, and 3) quantified the direct and indirect effects of fish herbivores and corallivores on juvenile corals. We found that macroalgae proliferated when herbivory was low but only in recently disturbed communities where coral cover was also low. When coral cover was < 10%, macroalgae increased 20-fold within one year under reduced herbivory conditions relative to high herbivory controls. Yet, when coral cover was high (50%), macroalgae were suppressed irrespective of the level of herbivory despite ample space for algal colonization. Once established in communities with low herbivory and low coral cover, macroalgae suppressed recruitment of coral larvae, reducing the capacity for coral replenishment. However, when we experimentally established small juvenile corals (2 cm diameter) following a disturbance, juvenile corals inhibited macroalgae from invading local neighborhoods, even in the absence of herbivore
MCR LTER: Coral Reef: Early life stage bottleneck determines rates of coral recovery following severe disturbance; Data for Speare et al., 2024, Ecology
The data included in this data package were collected on the north shore of Moorea, French Polynesia, from 2011-2018 to evaluate drivers of different recovery rates of corals at two depths (10m and 17m). Data on juvenile coral densities, growth, and mortality, were collected from annual time series photoquadrats. Data from two experiments on coral settlement tiles were used to evaluate how exclusion of fishes influences the density of coral recruits, and the survival of coral recruits at 10 and 17m. These data were used for analyses in the manuscript entitled "Early life stage bottleneck determines rates of coral recovery following severe disturbance". These data are in support of a publication Speare et al. (2024) Ecology. This material uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2024).
Network properties data and code used in "Ecological plasticity governs ecosystem services in multilayer networks".
<p>Code and network properties data used in the analyses presented in "Ecological plasticity governs ecosystem services in multilayer networks". Further information can be requested of the author David A. Bohan (David.Bohan@inrae.fr).</p>
Data and script: Community size can affect the signals of ecological drift and niche selection on biodiversity
<p>Updated version of the code. Data files are the same. This is the final version of the code, associated with a manuscript published in Ecology (doi: 10.1002/ecy.3014). A preprint is also available: https://www.biorxiv.org/content/10.1101/515098v1.abstract</p> <p>This is a unique dataset on insect communities sampled identically in a total of 200 streams in climatically highly different regions (100 in Brazil and 100 in Finland). The sampling design included 5 streams (communities) per watershed and provided us replicates of metacommunities (watersheds). Data also include information on in-stream variables (such as current velocity (m/s), depth (cm), stream width (cm), % of sand (0.25-2 mm), gravel (2-16 mm), pebble (16-64 mm), cobble (64-256 mm), and boulder (256-1024 mm), % of canopy cover by riparian vegetation, pH, conductivity, total nitrogen, and total phosphorus) and catchment level variables (such as average slope, % of native forest cover, pasture, agriculture, planted forests, urban areas, mining, water bodies, bare soil, secondary forest cover, and mixed land uses).</p> <p>In addition to the dataset, here we also provide and R code used to investigate the relationship between beta diversity and community size. This code calculates 4 types of beta-diversity metric for each of 100 watersheds (5 streams) in Brazil and Finland. Beta diversity: Sorensen and Bray-Curtis dissimilarity between all pairs. Beta deviation from null models: Raup-Crick (vegan version) and Bray-Curtis beta-deviation (based on the scripts by Chris Catano and Jonathan Myers). These beta diversity metrics are modelled against community size, environmental heterogeneity and spatial extent.</p> <p> </p>
Long time-series ecological niche modelling using archaeological settlement data.
<p><strong>CR_settlement_niche_[N]_[Yr]_[BC/AD].tif</strong></p> <p>Ecological niche models in GeoTIFF format generated with the MaxEnt software based using prehistoric settlement evidence as training data and environmental layers (elevation, mean annual precipitation, mean annual temperature, landscape water balance, soil types) as background data. Raster values represent the probability of presence of a settlement.<br> <strong>N</strong> - chronological ordering<br> <strong>Yr, BC/AD</strong> - calendar years BC or AD</p> <p> </p> <p><strong>CR_settlement_niche_combined.tif</strong></p> <p>All models combined by averaging.</p> <p> </p> <p><strong>CR_settlement_archeo.zip</strong></p> <p>Archaeological data used to train the MaxEnt models in ESRI SHP format with the following fields:</p> <p><strong>Site_Type:</strong> Cemetery or Settlement</p> <p><strong>Archeo_Dat:</strong> Archaeological dating (culture or period)</p> <p><strong>Source:</strong> Source dataset (AMCR or LONGWOOD)</p> <p>AMCR: Archeologická mapa České republiky – Archaeological Map of the Czech Republic. Retrieved from https://digiarchiv.aiscr.cz/.</p> <p>LONGWOOD: Kolář, J., Tkáč, P., Macek, M., & Szabó, P. (2016). Archaeology and Historical Ecology: the Archaeological Database of the LONGWOOD ERC Project. Archäologisches Korrespondenzblatt 46/4, 539-554.</p> <p><strong>Yrs_BP_Avg:</strong> Average dating in calendar years BP (based on the archaeological dating)</p> <p><strong>Yrs_BP_Unc:</strong> Temporal uncertainty of the dating (half of the culture or period's duration)</p> <p><strong>Loc_Accur:</strong> Spatial accuracy derived from the recorded degree of the accuracy of location (radius in meters around the center point)</p>
Data for: Seasonal dynamics of faunal diversity and population ecology in an estuarine seagrass bed
<p>These are the data used in the analyses described in the paper titled "Seasonal dynamics of faunal diversity and population ecology in an estuarine seagrass bed", accepted at Estuaries and Coasts. We acknowledge the tangata whenua for the rohe in which these data were collected, Ngāi Tārewa and Ngāti Īrakehu. We thank the Akaroa Taiāpure for their support of this research.</p> <p>The data included are:</p> <p>Raw count data of taxa for each tow, associated with additional metadata including the date of collection, tow coordinates, and estimated seagrass cover (MonthlyRawSampling_Duvauchelle_2020.csv). This data was put through cleaning steps outlined in the file docs/dataCleaning.Rmd prior to being used in any analyses.</p> <p>The cleaned community composition data (cleanedCommunity.csv), output from <a href="https://github.com/spflanagan/ecology-duvauchelle/blob/main/docs/dataCleaning.Rmd">docs/dataCleaning.Rmd</a> and used in the downstream community and population analyses.</p> <p>The GPS coordinates for the tows (gpsdat.csv). These were extracted from the raw data in the data cleaning process.</p> <p>NZsyngnathids_measurements.csv contains the measurements of the pipefish from images. These data also underwent a cleaning process documented in <a href="https://github.com/spflanagan/ecology-duvauchelle/blob/main/docs/dataCleaning.Rmd">docs/dataCleaning.Rmd</a>.</p> <p>The cleaned pipefish trait data (pipefishTraits.csv), output from docs/dataCleaning.Rmd and used in the downstream population analysis documented in <a href="https://github.com/spflanagan/ecology-duvauchelle/blob/main/docs/populationAnalyses.Rmd">docs/populationAnalyses.Rmd</a>.<br> </p>
Data from: A semi-automated approach to classify and map ecological zones across the dune-beach interface
<p>This is the raw data behind the publication: </p> <p><strong>A semi-automated approach to classify and map ecological zones across the dune-beach interface</strong></p> <p><strong>Abstract: </strong>Habitat classification and mapping underpins most conservation and management tools, because habitats are often used as a surrogate for all biodiversity. Some habitat boundaries are easy to delineate; however, sandy shores are ecotones or ecoclines given their dynamic interface between the marine and the terrestrial realms. Although methods for mapping habitats along shorelines have been broadly applied, we aim to test a semi-automated approach to mapping across-shore “sub-environments” in this transition zone at a finer scale. Using an empirical dataset of photographs covering a small area (three across-shore transects from each of two different areas) with a high resolution, we tested seven machine learning algorithms to determine which one had the best classification accuracy, and to identify which environmental variables are the main determinants of classifications. The randomForest, stochastic gradient boosting, and C5.0 algorithms most accurately classified the photographs as the correct sub-environment. Based on the randomForest algorithm, the variables entropy, drift cover rate, local slope, segmented vegetation cover and number of points with sand or marine litter had the highest influence on the classification. There was no sensitivity to spatial variation alongshore. This approach can be used to map sub-environments at larger scales using drone technology to capture georeferenced digital photographs systematically. Consequently, coastal habitats can be mapped at a finer scale without causing disturbance to this especially sensitive ecotone.</p>
Landscape and habitat data for Tetramorium ant species from Cordonnier et al. 2019 Landscape Ecology
<p>This README accompanies the file "data_Cordonnier_LandEcol.txt"</p> <p>Associated publication : </p> <p>Multi-scale impacts of urbanization on species distribution within the genus <br> <em>Tetramorium </em>- Landscape Ecology<br> M. Cordonnier, C. Gibert, A. Bellec, B. Kaufmann, G. Escarguel</p> <p> <br> ********************************** CONTENTS ***********************************<br> The data are in table form with TABs as variables field delimiters so they can <br> be readily imported in any statistical package or spreadsheet program. Please, <br> contact me if you need the file formatted otherwise. </p> <p>This file includes a description of the variables.</p> <p>The individuals described in this file were identified to species and analyzed for climate variables in</p> <p>Cordonnier, M., Bellec, A., Dumet, A., Escarguel, G., & Kaufmann, B. (2019). <br> Range limits in sympatric cryptic species: a case study in Tetramorium pavement <br> ants (Hymenoptera: Formicidae) across a biogeographical boundary. Insect <br> Conservation and Diversity, 12(2), 109-120.<br> </p> <p>*******************************************************************************<br> Variable names and descriptions</p> <p>ID Sample name<br> X Longitude in WGS 84 (World Geodetic System 1984) decimal degrees rounded to 5 decimal places<br> Y Latitude in WGS 84 (World Geodetic System 1984) decimal degrees rounded to 5 decimal places<br> SZ Name of the sampling area sensu Cordonnier et al. (2019)<br> SP Species identification based on mtDNA COI gene<br> PI10 Percentage of impervious surfaces within a 10 m buffer around the sample<br> PI30 Percentage of impervious surfaces within a 30 m buffer around the sample<br> PI500 Percentage of impervious surfaces within a 500 m buffer around the sample<br> MH1 Presence / absence of full soil with vegetation <br> MH2 Presence / absence of pavement <br> MH3 Presence / absence of unstabilized material (sand. gravel. compacted soil <br> with pebbles or small rocks) <br> MH4 Presence / absence of wood or root <br> MH5 Presence / absence of litter (woodchips or dead leaves) <br> MH6 Presence / absence of curb <br> MH7 Presence / absence of building <br> MH8 Presence / absence of feature (p.ex. lamp post. elec. pole. large rock) <br> MH9 Presence / absence of ditch or strong slope</p> <p>********************************* CONTACT **********************************<br> Please contact me at:</p> <p>Marion Cordonnier<br> e-mail: marion.cordonnier@hotmail.com</p> <p>*******************************************************************************<br> </p>
Coral growth data for the research article "Reconstruction of long-term sub-lethal effects of warming on a temperate coral in a climate change hotspot" in Journal of Animal Ecology
<p>This repository contains the coral growth data files used to generate the results for the following article:</p> <p> </p> <p>MJ. Vergotti, JP. D’Olivo, T. Brachert, P. Capdevila, J. Garrabou, C. Linares, P. Spreter, DK. Kersting (2024) Reconstruction of long-term sub-lethal effects of warming on a temperate coral in a climate change hot-spot. <em>Journal of Animal Ecology</em>. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2656.14225</p> <p> </p> <p><strong>Abstract: </strong>The impact of warming on zooxanthellate corals is widespread, from tropical to temperate seas, with their associated mortalities causing global concern. The temperate coral <em>Cladocora caespitosa</em> is the only zooxanthellate coral with reef-building capacity in the Mediterranean Sea, a climate change hotspot with warming rates triple the global average. Over the past two decades, <em>C. caespitosa</em> populations have suffered severe mortality events associated with marine heatwaves (MHWs). However, with monitoring efforts beginning, at best, in the 2000s, the occurrence of MHWs before to that period, as well as the sub-lethal effects of these events remain poorly understood. Here we use sclerochronology to reconstruct the histories of past stress events and long-term sub-lethal effects on <em>C. caespitosa</em> in three locations within the NW Mediterranean Sea, each with different environmental conditions. Skeletal extension, density and calcification rates were compared to the <em>in situ</em> seawater temperature of each site to assess their relationship. Additionally, we assessed the occurrence of skeletal growth anomalies to reconstruct stress events between 1991 and 2021, a period that encompasses the onset and evolution of warming-related mass mortality events in the NW Mediterranean Sea. Our results reveal a positive association between calcification and temperature, following a latitudinal temperature gradient. However, the evolution of the likelihood distribution of growth rates in the warmest site (Columbretes Islands) since the 1990s indicates a decrease in linear extension and calcification rates during the most recent years. With the increase in the frequency of MHWs and growth anomalies during the last decade, this decline suggests a recurrence in physiological stress events. These results unravel information on the long-term impacts of warming on coral growth and highlight the potential of applying sclerochronology to reconstruct sub-lethal effects of warming using <em>C. caespitosa</em>. </p> <p> </p> <p> </p> <p><strong>Funding</strong>: This research is supported by the Horizon 2020 program of research and innovation of the European Union under the MaCoBioS grant agreement, by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project no. 401447620) and by the Spanish Ministry of Science, Innovation and Universities under the project UndResCoral (project no. PID2022-137539OA-C22). D.K.K. was supported by a Ramon y Cajal postdoctoral grant funded by the Ministry of Science and Innovation (PEICTI 2021–2023; grant no. RYC2021-033576-I). C.L. acknowledges the support by ICREA Academia. J.G. acknowledges the grant “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S) funded by AEI 10.13039/501100011033.</p>
Data from: Ecological drivers and consequences of torpor in Andean hummingbirds
<p>This data package accompanies the paper "Ecological drivers and consequences of torpor in Andean hummingbirds", doi: 10.1098/rspb.2022.2099</p>
Supplementary data for "Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages of an intermittent stream"
<p><strong>Supplementary data for the Pozzi <em>et al.</em> paper entitled "Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic microbial assemblages and a tracking of exogenous bacterial taxa in a peri-urban intermittent stream".</strong></p> <p># Created by Dr Adrien C. MEYNIER POZZI on June, 29th, 2023<br> # Part of DOmic research project funded by the Agence de l’Eau - Rhône Méditerranée Corse [AE-RMC, Project 2020 0702 DOmic, 2020-2023], and of the DOmic extension funded by the EUR H2O'Lyon [ANR-17-EURE-0018] of Université de Lyon<br> # Part of the Chaudanne river long-term experiment site belonging to the Observatoire de Terrain en Hydrologie Urbaine (OTHU)<br> # Part of the work conducted in the team on Opportinistic Bacterial Pathogen in the Environment (BPOE) led by Dr. Benoit Cournoyer<br> # Samples were obtained in 2 campaigns, corresponding to periods before (2010-2011) or after (2018) the implementation of the 91/271/EEC European Directive that limited Combined-Sewer Overflow (CSO) discharges to the Chaudanne river<br> # Samples consisted in surface water, benthic and hyporheic sediments taken in run, riffle and pool geomorphologic features, either upstream or downstream the CSO outlet, plus positive and negative controls</p> <table> <tbody> <tr> <td><strong>Metadata. Name and description of data tables provided as supplementary information</strong></td> </tr> <tr> <td><strong>Data Name</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>Data S1. River hydrology variables and hydraulic gradients at surveyed transects</td> <td>Array to describe the hydrologic variables and gradients at the studied transects. Top line is header, second line is metadata for each recorded variable, and third line is the unit of the variable, if any.</td> </tr> <tr> <td>Data S2. Environmental variables (water physical-chemistry, nutrients, FIBs, MTEs, PAHs) with metadata</td> <td>An array to list environmental variables for all true samples (n=90) included in the study. Sample identifiers and dates are provided. First 8 rows list the CAS number, SANDRE number, unit, method, limit of quantification and norm for each variable, if any.</td> </tr> <tr> <td>Data S3. Hydrological indices and synthetic variables computed with ClustOfVar</td> <td>Hydrological indices computed for the river flow, precipitations and CSO overflows computed over a 3-week period preceding each sampling date.</td> </tr> <tr> <td>Data S4. Discharge events selected to compute CSO dilution ratios</td> <td>An array to describe CSO events included for the computation of the CSO dilution ratio (SI Data 6A) together with 6 tables and 3 figures (SI Data 6B to 6J) describing the CSO event ratio all year round over the studied period, as well as for events that occurred before or after the CSO was modified and during low flow or high flow season. In SI Data 6A, top line is header and second line is metadata for each recorded variable.</td> </tr> <tr> <td>Data S5. Raw environmental matrix for use in R</td> <td>An array to list experimental design and environmental variables for all true samples and controls. Several environmental variables were synthetized using the ClustOfVar method (Chavent et al (2012) 10.18637/jss.v050.i13). Format is directly usable in R software.</td> </tr> </tbody> </table> <p> </p>
Data for Hunting of sika deer over six decades does not restore forest regeneration, Journal of Applied Ecology
<p>Data used for Hunting of sika deer over six decades does not restore forest regeneration.</p>
Data and R code for “Individual-level variation in reproductive effort in chestnut oak (Quercus montana Willd.) and black oak (Q. velutina Lam.)”, Forest Ecology and Management, 2022
Masting is a population-level reproductive strategy, where individuals synchronize large but intermittent seed production. Despite the high degree of synchrony at the population level, there can be considerable variation in reproduction among individuals (intraspecific variation). Here, we use 18 years of acorn production data from individual chestnut oak and black oak from control and thinned stands, to understand what factors influence individual differences in reproductive effort and variability. We included a variety of tree-level measurements, environmental characteristics, and measurements from tree cores to determine if certain characteristics were associated variations in reproduction. We considered both mean annual acorn production per m2 crown and interannual variation in acorn production (CV) as response variables. We also classified individuals as super producers (i.e., those that consistently produce more acorns than others), good, fair and poor producers (i.e., those that consistently produce less or have a higher number of failure years). In chestnut oak, 14% of the individuals were classified as super producers and contributed 34% of the total acorns, while poor producers made up 35% of the trees and contributed only 16% to total acorn production. In black oak, super producers (14% of the individuals) contributed 31% of total acorns and poor producers (24% of the individuals) contributed only 9% of the acorns. Diameter at breast height (DBH) was the most consistent variable for explaining intraspecific variation in reproductive effort and variability (i.e., larger individuals had higher mean acorn production for both chestnut oak and black oak, and lower CV for black oak). Other variables that influenced reproduction and variation included elevation and clay content for chestnut oak, and slope for black oak. We found no significant effect from the thinning treatment on acorn production. Our results illustrate how tree-level and environmental characte
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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.