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107 results for “ecological dataset”
Interagency Ecological Program: Integrated Dataset of Phytoplankton Enumeration Data in the San Francisco Estuary, 1992-2024
Phytoplankton community composition is an important driver of zooplankton productivity and food supply for higher trophic levels in the San Francisco Estuary. Various monitoring surveys throughout the region collect phytoplankton enumeration data dating back to the 1990s. These include surveys from the CA Department of Water Resources (CADWR), CA Department of Fish and Wildlife (CDFW), the US Bureau of Reclamation (USBR), and the US Geological Survey (USGS). These surveys collect data via various sampling and laboratory methods which are not always directly comparable. This integrated dataset includes both enumeration counts and well-documented metadata to allow for informed decision-making in the integration of these data. It also standardizes taxonomic names between groups via a key list. Note that, in this dataset, we make conservative decisions about taxonomic resolution to ensure maximum compatibility between groups. For more detailed metadata and higher taxonomic resolution, refer to individual surveys’ publications or reach out to their primary contact.
LAGOS-NE Shallow Lakes: a dataset of lake variables and multi-scaled ecological context variables used to predict and compare trophic status and TP:CHLa relationships between shallow and non-shallow lakes in the Upper Midwest and Northeastern United States.
We conducted a macroscale study of 2,210 shallow lakes (mean depth ≤ 3m or a maximum depth ≤ 5m) in the Upper Midwestern and Northeastern U.S. We asked: What are the patterns and drivers of shallow lake total phosphorus (TP), chlorophyll a (CHLa), and TP–CHLa relationships at the macroscale, how do these differ from those for 4,360 non-shallow lakes, and do results differ by hydrologic connectivity class? To answer this question, we assembled the LAGOS-NE Shallow Lakes dataset described herein, a dataset derived from existing LAGOS-NE, LAGOS-DEPTH, and LAGOS-CLIMATE datasets. Response data variables were the median of available summer (e.g., 15 June to 15 September) values of total phosphorus (TP) and chlorophyll a (CHLa). Predictor variables were assembled at two spatial scales for incorporation into hierarchical models. At the local or lake-specific scale (including the individual lake, its inter-lake watershed [iws] or corresponding HU12 watershed), variables included those representing land use/cover, hydrology, climate, morphometry, and acid deposition. At the regional scale (e.g., HU4 watershed), variables included a smaller set of predictor variables for hydrology and land use/cover. The dataset also includes the unique identifier assigned by LAGOS-NE(lagoslakeid); the latitude and longitude of the study lakes; their maximum and mean depths along with a depth classification of Shallow or non-Shallow; connectivity class (i.e., whether a lake was classified as connected (with inlets and outlets) or unconnected (lacking inlets); and the zone id for the HU4 to which each lake belongs. Along with the database, we provide the R scripts for the hierarchical models predicting TP or CHLa (TPorCHL_predictive_model.R), and the TP—CHLa relationship (TP_CHL_CSI_Model.R) for depth and connectivity subsets of the study lakes.
Metabolism dataset: one year of high-frequency temperature, dissolved oxygen, wind, photosynthetically active radiation observations and low-frequency nutrient data for 58 lakes in the Global Lake Ecological Observatory Network
Understanding controls on primary productivity is essential for describing ecosystems and their responses to environmental change. Lake primary production is strongly controlled by inputs of nutrients and colored dissolved organic matter. While past studies have developed mathematical models of this nutrient-color paradigm, broad empirical tests of these models are scarce. We compiled data from 58 diverse and globally distributed and mostly temperate lakes to test such a model and improve understanding and prediction of the controls on lake primary production. These lakes varied widely in size (0.02-2300 km2), pelagic gross primary production (20-8000 mg C m-2 d-1), and other characteristics. The data package includes high-frequency dissolved oxygen, water temperature, wind speed, and solar radiation data as well as daily estimates of GPP and ER derived from those data. In addition, the data package includes median in-lake and stream concentrations of dissolved organic carbon and total phosphorus for a subset of 18 of those lakes.
Demographic, seed ecology, and range wide survey datasets for Chrysopsis highlandsensis 1999-2022
Chrysopsis highlandsensis (Highlands Goldenaster; Asteraceae) is a state endangered herb found primarily within pyrogenic scrub communities in south-central Florida. These datasets span 24 yrs of demographic monitoring across ten populations, 7 seed ecology experiments, and a repeated range wide survey conducted every 5 yr from 2005-2020.
Dataset and framework for the Open Potential Ecological Network of Tuscany
<p>This repository contains the main output of the related research, specifically: two Open Potential Ecological Networks (OPEN) of Tuscany in the Cytoscape format: "tuscany_potential_directed.cys" and "tuscany_potential_undirected.cys".</p> <p>Please see the "annotations.txt" file to more detailed explanation regarding the content in this repository.</p>
Networking nutrients: how nutrition determines the structure of ecological networks - Dataset
<p>Raw sequencing data and other metadata files are associated with Cuff et al. (2021a, 2022a), available at https://doi.org/10.5281/zenodo.4708418</p> <p>Data/code relating to the macronutrient contents and delineation of tropho-species clusters are associated with Cuff et al. (2021b, 2022b), available at https://doi.org/10.5281/zenodo.5738016</p> <p>Cuff, Jordan P. (2021a). A molecular analysis of the diet and biocontrol potential of spiders in cereal crops - Dataset. <em>Zenodo</em>. doi: 10.5281/zenodo.4708419</p> <p>Cuff, Jordan Patrick, Tercel, M. P., Vaughan, I. P., Drake, L. E., Wilder, S. M., Bell, J. R., … Symondson, W. O. (2021b). Evidence for nutrient-specific foraging of predators under field conditions. <em>Zenodo</em>. doi: 10.5281/zenodo.5738015</p> <p>Cuff, Jordan P., Tercel, M. P. T. G., Drake, L. E., Vaughan, I. P., Bell, J. R., Orozco-terWengel, P., … Symondson, W. O. C. (2022a). Density-independent prey choice, taxonomy, life history and web characteristics determine the diet and biocontrol potential of spiders (Linyphiidae and Lycosidae) in cereal crops. <em>Environmental DNA</em>, in press. doi: 10.1002/edn3.272</p> <p>Cuff, Jordan P., Tercel, M. P. T. G., Vaughan, I. P., Drake, L. E., Wilder, S. M., Bell, J. R., … Symondson, W. O. C. (2022b). Evidence for nutrient-specific foraging of predators under field conditions. <em>Authorea</em>. doi: 10.22541/au.164908092.21266343/v1</p>
LakeBeD-US: Ecology Edition - a benchmark dataset of lake water quality time series and vertical profiles
LakeBeD-US: Ecology Edition is a harmonized lake water quality dataset containing time series and vertical profiles of 21 lakes in the United States monitored by long-term monitoring institutions. These institutions include the North Temperate Lakes Long-Term Ecological Research program (NTL-LTER), Niwot Ridge Long-Term Ecological Research program (NWT-LTER), National Ecological Observatory Network (NEON), and the Carey Lab at Virginia Tech as part of the Virginia Reservoirs Long-Term Research in Environmental Biology (LTREB) site in collaboration with the Western Virginia Water Authority. The data include depth-discrete observations of 17 water quality variables including temperature, dissolved oxygen, chemical properties, Secchi depth, and more. Observations are divided into data collected by automated sensors at a relatively high temporal frequency and manually sampled data at a relatively low temporal frequency. All data were collected in situ. The data are available as Apache Parquet files, and the included R scripts give guidance on how to utilize and query the dataset in R. LakeBeD-US: Ecology Edition is an ecological science-oriented companion to LakeBeD-US: Computer Science Edition. The Computer Science Edition is available on the Hugging Face Hub.
Dataset: Multi-level network dataset of social-ecological interdependencies in ten Swiss wetlands based on qualitative interviews and quantitative surveys
<p>The dataset originated from quantitative online surveys and qualitative expert interviews with organizational actors relevant to the governance of ten Swiss wetlands from 2019 till 2021. Multi-level networks represent the wetlands governance for each of the ten cases. The collaboration networks of actors form the first level of the multi-level networks and are connected to multiple other network levels that account for the social and ecological systems those actors are active in. 521 actors relevant to the management of the ten wetlands are included in the collaboration networks; quantitative survey data exists for 71% of them. A unique feature of the collaboration networks is that it differentiates between positive and negative forms of collaboration specified based on actors' activity areas. Therefore, the data describes not only if actors collaborate but also how and where actors collaborate. Further additional two-mode networks (actor participation in forums and involvement in other regions outside the case area) are elicited in the survey and connected to the collaboration network. Finally, the dataset also contains data on ecological system interdependencies in the form of conceptual maps derived from 34 expert interviews (3-4 experts per case).</p>
A Dataset for Investigating Socio-ecological Changes in Arctic Fjords v2
<p>The collection of in situ data is generally a costly process, with the Arctic being no exception. Indeed, there has been a perception that the Arctic lacks for in situ sampling; however, after many years of concerted effort and international collaboration, the Arctic is now rather well sampled with many cruise expeditions every year. For example, the GLODAP product has a greater density of in situ sample points within the Arctic than along the equator. While this is useful for open ocean processes, the fjords of the Arctic, which serve as crucially important intersections of terrestrial, coastal, and marine processes, are sampled in a much more ad hoc process. This is not to say they are not well sampled, but rather that the data are more difficult to source and combine for further analysis. It was therefore noted that the fjords of the Arctic are lacking in FAIR (Findable, Accessible, Interoperable, and Reusable) data. To address this issue a single dataset has been created from publicly available, predominantly in situ data from a number of online platforms. After finding and accessing the data, they were amalgamated into a single project-wide standard, ensuring their interoperability. The dataset was then uploaded to PANGAEA so that it itself can be findable and reusable into the future. The focus of the data collection was driven by the key drivers of change in Arctic fjords identified in a companion review paper. After receiving feedback on this process and the dataset itself, a second version (v2.0) has been created.</p>
Dataset and code Petry et al. 2018 Journal of Ecology
<p>This dataset contains all the data and code needed to reproduce the analyses in</p> <p>Petry, W.K., G.S. Kandlikar, N.J.B. Kraft, O. Godoy, & J.M. Levine (2018) A competition-defence trade-off both promotes and weakens coexistence in an annual plant community. Journal of Ecology. DOI: 10.1111/1365-2745.13028</p> <p>Complete metadata is provided in README.md</p>
Spatial dataset for ecological niche and spatial distribution modeling of Herichthys bartoni (Cichliformes: Cichlidae) in the Media Luna spring, Mexico
<p>Dataset for the endangered endemic cichlid <em>Herichthys bartoni</em> in the Media Luna spring, Mexico. This data includes occurrences records by species life stage (adult, juvenile and fry), in three field sessions corresponding to the summer period, in the years 1999, 2009 and 2019.</p> <p>For more information about the codes where the previous datasets could be used, visit the following repository with URL: <a href="https://doi.org/10.5281/zenodo.7603557">https://doi.org/10.5281/zenodo.7603557</a>.</p> <p>Likewise, the UC and WDp variables used to run the ecological niche and spatial distribution model, by summer period, can be found in the following repository wirh URL: <a href="https://doi.org/10.5281/zenodo.7603890">https://doi.org/10.5281/zenodo.7603890</a>.</p>
The 30 m land cover dataset for capturing land cover changes induced by ecological restoration from 1990 to 2022 on the Chinese Loess Plateau
<p>Continuous time-series of land cover is critical for attributing runoff, sediment and carbon changes on the Chinese Loess Plateau (CLP). However, current land cover products with annal temporal resolution lack spatial identification accuracy, particularly in capturing authentic changes of cropland, forest and grassland. To address these issues, a 30 m annual land cover dataset was proposed by the Yellow River Conservancy Commission (YRCC_LPLC) for the CLP from 1990 to 2022. Different levels of land cover were classified using different combinations of spectral, monthly and annual temporal and topographic features and Random Forest classifier. Compared to other land cover products (45.64%–73.38%), the accuracy of YRCC_LPLC has a better performance with an overall accuracy of 85.16%. The YRCC_LPLC is capable of capturing not only the explicit spatial variation but also the change direction and change time of land cover, especially for the most critical conversion of cropland into forest and grassland induced by implementation of Grain to Green Program on the CLP.</p>
Dataset from University of Idaho 2004, master's thesis [Littoral ecology of epilithic algae in the Rocky Reach Pool, Mid-Columbia River (Washington State) - The effects of reservoir fluctuations.]
(Abstract from thesis) Epilithic algae, water column physical/chemical properties, and sediments were examined in the impounded Mid-Columbia River including the Rocky Reach Reservoir. Primary objectives included determination of the effects reservoir drawdown has on epilithic algae and potential nutrient enrichment via sediment. Epilithic algae were analyzed by pigment concentration, gravimetrically, and species composition. Reservoir elevation fluctuated at higher rates at tailrace sites (0.41-0.25 m/hr) compared to the forebay site (0.06-0.08 m/hr). Littoral exposure times were also greater at tailrace sites (mean of 8 hrs compared to 0 hr at the forebay site). Mean epilithic algae monochromatic chlorophyll a over all sampling periods at mainstem sites was 76.7 ± 4.8 mg/m2 (95 % C.I.). Epilithic algae monochromatic chlorophyll a in the zone of water fluctuation (0-1 m) was less at Wells tailrace (38.8 mg/m2) compared to Rocky Reach forebay (141.3 mg/m2) during summer, 2000 and 2001. Mean epilithic biofilm ash-free oven-dry weight over all sampling periods at mainstem sites was 25.6 ± 1.5 g/m2 (95 % C.I.). Mean autotrophic index across all mainstem locations was 439 indicating a large heterotrophic component within the epilithic biofilms. Epilithic algae communities were dominated by diatoms (50.2 %) and cyanobacteria (35.9 %), with some green algae (13.8 %). Canonical correlation analysis indicated that temperature, depth, site, and the water elevation change rate were important controllers of epilithic algae chlorophyll pigments. Mean textural characteristics of dredged sediment were 51.1 % sand, 43.2 % silt, and 5.7 % clay. Mean organic matter content in this sediment was 4.1 %. The mean seston sedimentation rate across mainstem locations was 11.3 g m-2 d-1 and organic matter comprised 14.7 % of the material collected from the water column.
Supplementary script and datasets for Lami et al. (2020), Ecology Letters
<p>This repository includes an example script for the Agreement Metric as well as the script and datasets (.csv files) necessary to run the models described in the paper "Species-habitat networks elucidate landscape effects on habitat specialization of natural enemies and pollinators" (Lami et al., 2020) - Ecology Letters.</p>
Dataset from Pardini, E. A., Parsons, L. S., Ştefan, V., & Knight, T. M. (2018). GLMM BACI environmental impact analysis shows coastal dune restoration reduces seed predation on an endangered plant. Restoration Ecology, 26(6), 1190-1194.
<p>Data and its metadata used in the analysis from the publication: Pardini, E. A., Parsons, L. S., Ştefan, V., & Knight, T. M. (2018). GLMM BACI environmental impact analysis shows coastal dune restoration reduces seed predation on an endangered plant. Restoration Ecology, 26(6), 1190-1194. <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/rec.12678">https://onlinelibrary.wiley.com/doi/full/10.1111/rec.12678</a> </p>
Supporting dataset for manuscript "Estimating the microarthropod diversity in cropping systems by comparing ecological indices across Europe" by Bigiotti et al. 2025
<p>This dataset contains counts of mesofauna individuals classified as Biological Forms (BF). It represent the raw data used for all indices calculation in the manuscript entitled "Microarthropod communities' diversity for soil health assessment: comparing several ecological indices across Europe" by authors Gaia Bigiotti, Francesco Vitali, Stefano Mocali, Giovanni L’Abate, Eligio Malusà, Dawid Kozacki, Irena Bertoncelj, Morgane Ourry, Massimo Pugliese, Heinrich Maisel, Expedito Olimi, Maria Grazia Tommasini, Carlo Jacomini, and Lorenzo D’Avino.</p>
Datasets of the Doctoral Dissertation: "A Geoarchaeological Approach to the Materiality and Historical Ecology of Earth Mounds: The Colina da Monte Site, Uruguay."
<p>These PDF files contain the datasets, workflows, and codes from Rocío M. López Cabral's Doctoral Dissertation project: "A Geoarchaeological Approach to the Materiality and Historical Ecology of Earth Mounds: The Colina da Monte Site, Uruguay."</p>
Dataset underpinning "Understanding health behaviours in context: A systematic review and meta-analysis of Ecological Momentary Assessment studies of five key health behaviours"
<p>This is the dataset underpinning the article "Understanding health behaviours in context: A systematic review and meta-analysis of Ecological Momentary Assessment studies of five key health behaviours": https://pubmed.ncbi.nlm.nih.gov/35975950/</p>
Synthesizing Multiple Long-Term Datasets to Test Flow Ecology Relationships
<p>This database is comprised of time series of fish abundances at stream and river sites across the contiguous United States, along with associated hydrologic and land cover metrics. The database has been assembled in order to test hypothesized fish flow-ecology relationships across diverse species assemblages and riverine contexts. Methods for compilation of the database and additional information can be found in two accompanying files: "SynthesizingDatasetsForFlowEcology_v1_0_0.pdf" contains detailed methodology and results, and "ReadMe_FishFlow_v1_0_0.csv" contains information about the variables found within each database file. This project was funded by a US Army Corps of Engineers contract to the US Geological Survey, with a subcontract to the University of Georgia. Please note, the contract number for this project is G21AC10482, not G21AS00529 as is stated in the summary document (SynthesizingDatasetsForFlowEcology_v1_0_0.pdf).</p>
Datasets and Codes for Purgar et al. 2022: Quantifying research waste in ecology
<p>This is a Data package containing Datasets and Codes to reproduce the analyses and create figures for the paper Purgar et al. 2022: Quantifying research waste in ecology. Datasets include the original effect sizes as extracted from studies and the final set of the effect sizes used in the meta-analysis. The code includes the code used to perform meta-analysis and to create plots (in the main article and the supplementary files). Description of the files and variables can be found in the Readme file.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.