Find research datasets worth reusing

openCC (other)Mar 2023View details →

Environmental and biological data associated with captive-reared Delta Smelt Study, Sacramento-San Joaquin Delta, CA, January-March 2019

The endangered Delta Smelt Hypomesus transpacificus is an osmerid fish endemic to the upper San Francisco Estuary. A captive breeding program for the species led by the Fish Culture and Conservation Laboratory (FCCL), University of California, Davis, began in 1996 to create a refuge population. In order to better understand how captive Delta Smelt would fare in conditions outside of the hatchery, we placed captive-reared fish in enclosures in the Sacramento San-Joaquin Delta, and evaluated their ability to survive, feed, and maintain condition. Fish were acclimated in the hatchery at FCCL, tagged, swabbed, weighed, measured, and transferred to enclosures in the field. There were three types of enclosures (n=2 for each type), varying in mesh size and wrap condition. In January 2019, 384 adult Delta Smelt (243 days post hatch) were transferred to enclosures in Rio Vista. In February 2019, 360 adult Delta Smelt (278 days post hatch) were transferred to enclosures in the Deepwater Shipping Channel. For each deployment, fish remained in enclosures for approximately one month, then were retrieved from enclosures, euthanized, identified, weighed and measured. A subset were also analyzed for diet contents. During the one-month long deployments, cages were checked for biofouling, damage, and dead fish, and water quality measurements and zooplankton samples were collected.

openCC (other)May 2023View details →

Ecosystem metabolism and associated environmental data for a forested, meadow and reforested reach of White Clay Creek, Chester Co., Pennsylvania; 1971-1975 and 1997-2010

Ecosystem metabolism data for a 3rd-order Piedmont stream were collected during two periods: P1- April 1971 – Dec 1975, and P2- May 1997 – January 2010. Measures were made in a meadow and a forested reach during each period and in a reforested (formerly meadow) reach during the latter years of P2. During P1, measures were made by transferring streambed substrata to chambers in water jackets located on the streambank and measuring dissolved oxygen changes over diel periods. During P2, open system measures of dissolved O2 change were made for several days in warm and cold seasons, with reaeration determined from a propane injection experiment. Metabolism estimates were determined from diel curves of dissolved O2 change. Photosynthetically active radiation (PAR) and chlorophyll were measured concurrent with many measurements in P1 and all measures during P2, and temperature with all measures. Water chemistry parameters (NH4-N, NO3-N, PO4-P, SiO2, Cl, SO4, total alkalinity, pH) associated with each run are included in the data set, as are days since storm of various thresholds. Field procedures, analytical methods and data analyses are detailed in Bott, T.L. & J. D. Newbold, 2023. A multi-year analysis of factors affecting ecosystem metabolism in forested and meadow reaches of a Piedmont Stream. Hydrobiologia

openCC0Jan 2026View details →

Summary of tundra pond zooplankton and associated environmental data from the Barrow, AK IBP tundra ponds (1970s & 2010s)

A comparison of historic (1970s) and more recent (2010s) zooplankton and environmental data from Arctic tundra ponds near Utqiaġvik, AK has given us valuable insight into changes in zooplankton communities that have occurred in recent times.

openCustomApr 2022View details →

Periphyton and Associated Environmental Data Relative from Samples Collected from the Greater Everglades, Florida, USA from September 2005 to November 2014

This data package contains peripihyton and environmental data collected annually during the wet season between 2005 and 2014 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units and each year, random coordinates are 'drawn' within each PSU and one sampleable draw is visited in each. Sampled periphyton is processed for diatoms, slides are prepared, and 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental, periphyton biomass, and soft algal abundance datasets.

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Metagenome-Assembled Genomes Abundance & Activity Tables. Environmental Parameters Associated with the dataset.

Lake Mendota, WI, USA, is a temperate lake subject to annual temperature and oxygen fluctuations. Each summer, the water column becomes anoxic (no-oxygen). In 2020, we sampled the lake at weekly intervals, at different depths (5, 10, 15, 20 and 23.5m). For each time+depth sample, we collected metagenomes, viromes and metatranscriptomes. Environmental data profiles were collected on-site for each sampling day.  Following standard metagenomic binning best practices, we obtained 431 metagenomes-assembled-genomes (MAGs). This record comprises the microbial abundance and expression table for these MAGs, and the environmental profiles collected each day.

opencc-by-4.0Nov 2024View details →

zenodo48/100

Environmental data associated to particular health events example dataset

The data represents and example output for environmental data (i.e. climate and pollution) linked with individual events through location and time. The linkage is the result of a semantic query that integrates environmental data within an area relevant to the event and selects a period of data before the event. The resulting event-environmental linked data contains: <ul> <li>The data for analysis as a data table (.csv) and graph (.ttl)</li> <li>The metadata describing the linkage process and the data (.csv and .ttl)</li> <li>The interactive report to explore the (meta)data (.html)</li> </ul> The graph files are ready to be shared and published as Findable, Accessible, Interoperable and Reusable (FAIR) data, including the necessary information to be reused by other researchers in different contexts.

opencc-by-4.0Mar 2022View details →

edi48/100

Periphyton Abundance and Structural Traits, Diatom Taxa Relative Abundance, and Associated Environmental Data from Samples Collected from the Greater Everglades, Florida, USA from September 2005 - ongoing

This data package contains benthic algae (periphyton) and environmental data collected annually during the wet season between 2005 and 2021 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan (CERP MAP) intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units (LSU) and each year, random coordinates are 'drawn' within each PSU and one draw is visited in each sampleable PSU. Sampled periphyton is processed for aggregate structural traits (i.e., biomass, chlorophyll-a, organic content, and phosphorus concentration) and for diatom taxa. For diatoms, slides are prepared, and at least 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental and spatial data for each sampled draw. In addition to the CERP MAP data, this dataset also includes data on the same variables collected from up to 21 primary sampling units in the Broward County Water Preserve Area beginning in 2020. The data in this package replace and supersede those in package knb-lter-fce.1210 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1210).

openCC (other)Sep 2025View details →

zenodo44/100

Isotopes and related data associated with water tracing with environmental DNA in a high-Alpine catchment

Isotopes and related data associated with water tracing with environmental DNA in a high-Alpine catchment Prepared by Natalie Ceperley, February 2020.   All methods associated with this data are available in the manuscript: Elvira Mächler, Anham Salyani, Jean-Claude Walser, Annegret Larsen, Bettina Schaefli, Florian Altermatt, and Natalie Ceperley.  2019.  Water tracing with environmental DNA in a high-Alpine catchment, Hydrology and Earth System Sciences. https://doi.org/10.5194/hess-2019-551.  Related data sets are and will be published in the Vallon de Nant Community on Zenodo. Associated sequencing data are publicly available on European Nucleotide Archive (Mächler et al., 2020).  All isotope data analyzed in the laboratory of Torsten W. Vennemann at the University of Lausanne.    All Files:     ▪    NaN - No measurement or sample     ▪    Details regarding measurement are available in paper or supplement.   Files:  1)    climate_hydro_2017_daily.csv      ⁃    16 columns:          ⁃    1. day of year with January 1, 2017 = 1         ⁃    2-5. Q: daily mean, min, max, and baseflow discharge as measured at outlet (location ER/MR), in liters / day          ⁃    6. P: mean mm of rain across catchment per day         ⁃    7. SR: total solar radiation per day in W/hr/m2 as median of 4 meteorological stations         ⁃    8-10. SCA: mean, min, and max snow covered area on days with satellite imagery available for whole catchment area, in %         ⁃    11-13. water temperature, mean, min, and max, at outlet (location ER/MR), in degrees C         ⁃    14-16. air temperature, mean, min, and max at 4 meteorological stations, in degrees C 2)    delta-18-O_permil.csv      ⁃    stable isotopes of water (delta 18-O) in per mil     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 3)    delta-2-H_permil.csv      ⁃    stable isotopes of water (delta 2-H) in per mil     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 4)    dqdt_outlet_prev48hrs.csv     -    dq/dt determined at the outlet for the previous 48 hours at sampling moment (TimeOfSamples_HR.csv) for each sampling site     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 5)    ednasamplecount.csv      -    this is the tally of samples (1 sample includes 4 replicates)     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 6)    electricalconductivity_instrument.csv      ⁃    Code:              108 - post-analyzed using a glass bodied 6 mm probe in the laboratory (Jenway  4510, Staffordshire, UK).              102 - hand measurement with WTW (multi-3510 with a  IDS-tetracon-925, Xylem Analytics, Germany)     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 7)    electricalconductivity_uScm.csv      -    this is the electrical conductivity in micro siemens per cm, according to the instruments coded in electricalconductivity_instrument.csv     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 8)    LC-excess.csv      -     this is the line control execss from the meteoric water line as determined by the samples in the file: precipitationistopemetadata.csv     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 9)    locations.csv      ⁃    Location codes used in other files.      -    Coordinates in CH1903 / LV03 and WGS 84 (lat/lon). Elevation in m. asl.  10)    precipitationisotopemetadata.csv      -     This is the sampling information for the isotope data that was used to calculate the meteoric water line.      -    The full data set will become available in a subsequent publication on Zenodo linked to the same community.      -    4 columns:          -    1. code: rain (1) or snow (2)         -    2. collection date and time         -    3. elevation in m. asl.          -    4. in the case of rain, this is the depth of collection in mm (area normalized volume), in the case of snow, this is the mean depth below the surface that the sample was taken from in cm.      ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 11)    sampledates.csv      -    These are the sample dates in day, month, year and day of year corresponding to the rows in other files 12)    stationlocations.csv     -     These are the locations of four meteorological stations and discharge measurement station.      -    Coordinates in CH1903 / LV03 and WGS 84 (lat/lon). Elevation in m. asl.  13)    TimeOfSamples_HR.csv      -    This is the time of the sample in hours and decimals correspond to minutes past hour     ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv) 14)    watertemperature_degC.csv      ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv)     -     measure in degrees C     -     instrument in watertemperature_instrument.csv 15)    watertemperature_instrument.csv      ⁃    Code:              1 = hand measurement with WTW (multi-3510 with a  IDS-tetracon-925, Xylem Analytics, Germany)             2 = HOBO Pendant Temperature/Light Data Logger 64K - UA-002-64", Onset (Bourne, MA, USA)             3 = Continually logging WTW (IDS-tetracon-325, Xylem Analytics, Germany)             4 = Continually logging (10min) HOBO U24-001 Conductivity, Onset (Bourne, MA, USA)      ⁃    columns correspond to sampling locations (locations.csv), rows correspond to sampling days (sampledates.csv)

opencc-by-4.0Dec 2018View details →

edi44/100

CO2, CH4, and H2O flux data and associated environmental variables for the BBC collapse scar for 2004

This data set contains flux measurements for the transect from the center of the BBC collapse scar (0m) into the surrounding fire scar (30m) of the Survey Line Fire (burned in June-July 2001). We measured CO2, H2O and CH4 fluxes every one to two weeks throughout the growing season of 2004. We measured fluxes at permanent plots established from the center of the bog into the surrounding burn at 0, 6, 12, 18, 24, and 30 m on the east and west side of the transect. Flux measurements on either side of the transect were treated as replicates. CO2 and H2O fluxes were measured using a Li-840 infrared gas analyzer (Licor Inc., Lincoln, NB, USA). The IRGA was calibrated before each trip to the field using a span of 400 ppm and a zero of N2 gas. We logged data every 0.5 seconds for 2 min. To account for measurement variability, we conducted two measurements in succession at each location, after flushing the chamber for accumulated CO2 and H2O. For the flux measurements, we built plexiglass chambers with pipe insulation bases with dimensions of 61 x 61 x 30.5 cm, 61 x 61 x 61 cm, or 61 x 61 x 122 cm. The shorter chambers were used in the collapse portion of the transect. Chambers included fans for air circulation, inlet and outlet ports for CO2 measurements, or just outlet ports for CH4 measurements (Carroll and Crill 1997). We placed chambers directly on the soil surface and used pipe insulation and plastic sheeting to make a solid seal during the measurement. To estimate the volume for each chamber measurement, we measured the distance to the soil surface from a 6 cm grid suspended 30 cm above each plot, the surface area was then used to calculate the chamber volume for each measurement. Dark measurements were used to determine CO2 derived from soil and root respiration (ecosystem respiration) using a two-layer cloth shroud with a reflective surface to exclude solar radiation. To estimate net ecosystem exchange (NEE) of CO2, we conducted chamber measurements of plant and soi

openOpenNov 2005View details →

dryad40/100

Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities

Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by the environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. For this purpose, we generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high Arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more likely reflect interactive associations. Our results indicate that positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.

opencc-zeroJul 2020View details →

Fig. 3 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 3. Response curves of three morphological variables of Piaractus mesopotamicus (proportion of increase) respect to dissolved oxygen gradient. Black arrow indicates the DO concentration determined for the inflection point of the reaction norm.

Fig. 1 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 1. Development and reversion of the three morphological variables exposed to nine hours of hypoxia, followed by three hours of normoxia in Piaractus mesopotamicus. (a) lower lip, (b) maxillary, and (c) opercular valve. Capital letters above box plots indicate groups in multiple comparisons (Tukey's tests) after repeated measures ANOVA.

Fig. 4 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 4. Response curves of behavioral and respiratory variables of Piaractus mesopotamicus respect to dissolved oxygen gradient. Black arrow indicates inflection point given by the four parameters logistic function. The curve fitted to data points is not shown for horizontal and vertical movements due to the great dispersion.

Fig. 5 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 5. Comparisons of plasticity among behavioral (a), respiratoy (b) and morphological traits (c) of Piaractus mesopotamicus as measured by the coefficient of variation (CV) across the DO gradient. Capital letters above box plots indicate groups in multiple comparison Tukey's tests after a one way ANOVA. Names of traits as defined in the text.

Fig. 2 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 2. Photographs showing increases in size of the three morphological traits of Piaractus mesopotamicus analyzed exposed to extreme hypoxia: (a) lower lip, (b) maxillary, and (c) opercular valve. White arrow indicates the area where the expansion of dermal tissue occurred.

opencc-zeroDec 2015View details →

dryad40/100

Data from: Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri

Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations. We analysed new SNP data of 444 plants with the same methodology (partial Mantel tests, PMTs) as in the original study and additionally with a latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41% (PMTs) and 51% (LFMM) were associated with environmental factors in the independent data set. However, only 5% (PMTs) and 15% (LFMM) of the associations showed the same environment–allele relationships as in the original study. In total, we found 11 genes (31%) containing the same association in the original and independent data set. These can be considered prime candidate genes for environmental adaptation at a broader geographical scale. Our results suggest that selection pressures in highly heterogeneous alpine environments vary locally and signatures of selection are likely to be population-specific. Thus, genotype-by-environment interactions underlying adaptation are more heterogeneous and complex than is often assumed, which might represent a problem when testing for adaptation at specific loci.

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Data from: Environmental variation associated with topography explains butterfly diversity along a tropical elevation gradient

Few studies have evaluated the role of topography on the diversity patterns of biological communities along elevation gradients. We evaluated the influence of microclimate and vegetation structure associated with topographic variation on the richness and composition of species of different families of butterflies on a mountain located in a dry enclave (Chicamocha River Canyon) in the northern Andes, Colombia. We captured butterflies over four months at 18 elevations (300 to 1500 m a.s.l.) in two topographic positions (riverbed and hillslope) using an entomological net and traps baited with fermented fruit. In general, butterfly richness increased with elevation in both topographic positions. However, the richness-elevation relationship changed with butterfly family. The riverbed and hillslope sites host different assemblages of butterflies, and this pattern that was consistent for most families. In the riverbed, two sets of species are recognized along the elevation gradient (one below 700 m a.s.l. and the other above 1000 m a.s.l.), mainly owing to species replacement. On the hillslopes there was no clear pattern of grouping associated with elevation. Microclimate differences between the riverbed and hillslope sites along the elevation gradient were related to the vegetation structure and explained the variation in butterfly species composition. Our results highlight the role of topography not only by explaining the response of species richness and composition to environmental variation determined by elevation, but also as a factor that must be considered in the planning and management of biodiversity conservation in the mountains.

opencc-zeroNov 2021View details →