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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.
Sherbo et al. 2023 Data Package. Data associated with study assessing effects of dissolved organic matter on phytoplankton productivity in boreal lakes. The majority of data was collected in 2018 at the IISD Experimental Lakes Area in Northwestern Ontario
Allochthonous dissolved organic matter (DOM) structures many physical, chemical, and biological properties of lakes, including key variables that control productivity at the base of freshwater food webs. We examined phytoplankton biomass and productivity and their drivers, across eight pristine boreal lakes with DOM ranging from 3.5 to 9.5 mg DOC L-1. Increases in DOM were associated with significant increases in epilimnetic nitrogen, phosphorus and chlorophyll a (Chl a) concentrations suggesting that nutrients associated with DOM stimulate phytoplankton biomass and productivity. Such results were misleading; there was no significant relationship between Chl a and phytoplankton biomass measured via microscopy, and results did not incorporate the effects of DOM on thermocline and euphotic depth. Chl a:biomass and Chl a: carbon ratios indicated that increases in Chl a with DOM were driven by photo-acclimation to declining light availability. Increases. Further, increases in DOM led to large declines in thermocline (~50 %) and euphotic (~75 %) depths, and depth-integrated phytoplankton biomass and primary production (~70 %).
CoRRE Trait Data: A collection of 17 categorical and continuous traits for more than 4000 grassland species worldwide
In our changing world, it is critical to understand and predict plant community responses to global change drivers. Plant functional traits promise to be a key predictive tool for many ecosystems, including grasslands, however their use requires both complete plant community and functional trait data. Yet, representation of these data in global databases is incredibly sparse, particularly beyond a handful of most used traits and common species. Here we present the CoRRE Trait Database, spanning 17 traits (9 categorical, 8 continuous) anticipated to predict species’ responses to global change for 4,079 vascular plant species across 173 plant families present in 390 grassland experiments from around the world. The database contains complete categorical trait records for all 4,079 plant species, obtained from a comprehensive literature search. Additionally, the database contains nearly complete coverage (99.97%) of species mean values for continuous traits for a subset of 2,927 plant species, predicted from observed trait data drawn from TRY and a variety of other plant trait databases using Bayesian Probabilistic Matrix Factorization (BHPMF) and multivariate imputation using chained equations (MICE). These data will shed light on mechanisms underlying population, community, and ecosystem responses to global change in grasslands worldwide.
Hourly meteorological data gapfilled for sensor downtimes collected near Toolik Field Station, Alaska, summers 2012-2016
This data set includes meteorological parameters collected near Toolik Field Station from 2012 to 2016 under National Science Foundation (NSF) Office of Polar Programs ARC 0908444 (to Laura Gough), ARC 0908602 (to Natalie Boelman), and ARC 0909133 (to John Wingfield). It also includes meteorological data collected by two additional entities that are available on public repositories. Toolik data reflect data collected by the Toolik Envronmental Data Center and Imnavait data reflect data collected by the Arctic Observatory Network (AON). These data have been modified such that that sensor downtimes have been gapfilled by pulling data from the next nearest station. These data are associated with publication DOI: 10.1111/jav.01712
Carbon dioxide response curve, dark respiration, specific leaf area, and leaf nitrogen data for the 2014 Eriophorum vaginatum reciprocal transplant gardens at Toolik Lake and Sagwon, AK, collected in 2016.
Transplant gardens at Toolik Lake and Sagwon were established in 2014. At each location, 60 tussocks each from ecotypes of Eriophorum vaginatum from Coldfoot (CF, 67°15′32″N, 150°10′12″W), Toolik Lake (TL, 68°37′44″N, 149°35′0″W), and Sagwon (SAG, 69°25′26″N, 148°42′49″W) were transplanted. Half the transplanted tussocks were grown under ambient conditions, while the other half were exposed to passive warming supplied by open-top chambers (OTC). Data were collected in late June through July 2016 include carbon dioxide response curve data, dark respiration, specific leaf area, and leaf nitrogen content.
Meteorological data collected on Toolik Lake during the ice free season for 2010-2012, Arctic LTER, Toolik Research Station, Alaska
File describing the metological conditions on Toolik Lake (named the Toolik Lake Climate station), adjacent to the Toolik Field Research Station (68 38'N, 149 36'W). This is a floating climate station and should not be confused with the Toolik Field Station Climate site (TFS Climate Station or Met Station) which is a terrestrial station (located on land). Note that this land station has been called the "Toolik Main Climate Station", and the station on the lake is located where the main lake sampling site is located so it has also been called the Toolik Lake Main Climate Station. Measurements include air temperature, relative humidity, wind speed and direction, and radiation.
Fire Self-Limitation (FiSL) Experiment: Quantifying Wildfire Carbon Combustion Losses in boreal Deciduous and Mixed Forests in Interior Alaska and the Boreal Cordillera IX: metrics derived from All Raw Data Collected Plus Data from Previous Studies on the 2004 Alaska Wildfires Included in Analysis 2022
This data set includes metrics derived from field and lab data collected for deciduous and mixed deciduous-confier plots collected in the summer of 2022 (Shovel Creek (2019), Aggie Creek (2015), Hess Creek (2019), Baker (2015), Munson Creek (2021), Isom Creek (2020), 2019MA014 (2019), and 2019BC005 (2019)), as well as additional data for conifer plots from previous studies of the Taylor Highway Complex (2004), Dall Creek/Yukon Crossing (2004), and Boundary (2004) fires. Those additional data were acquired from: https://www.lter.uaf.edu/d1/d1-detail/id/773 and https://daac.ornl.gov/ABOVE/guides/ABoVE_Plot_Data_Burned_Sites.html. From this complete data set of 333 plots, 311 plots were used in analyses in Black at al. (NCC) paper: "Increased deciduous tree dominance reduces wildfire carbon losses in boreal forests". Plots excluded (from 2022 FiSL data) were poplar-dominated, mixed poplar/conifer dominated, missing soil C data, or conifer-dominated (adventituous root heights were not recorded consistently at sites in 2022 making it impossible to estimate pre-fire conifer stand organic soil C pools for 2022-collected conifer plots). Only 2005-collected conifer plots were used in NCC paper analyses. For all plots, in addition to field/lab derived site characteristics and combustion metrics, post hoc remotely sensed metrics were derived: pre-fire NDVI/EVI-2 trends, 1980-2010 climate normals, and DOB weather metrics.
Biogeochemical data collected from Northeast Shark Slough, Everglades National Park (FCE LTER) from September 2006 to September 2008
Each site's physical characteristics (pH, water depth and temperature) were measured in the field and recorded. Two water samples (filtered and unfiltered) were collected from each throw, along with a floc sample (if present). All samples were taken back to the lab for analysis (e.g. water content, % organic matter, bulk density, and TP/TN/TC).
Macrophyte count data collected from Northeast Shark Slough, Everglades National Park (FCE LTER) from September 2006 to September 2008
Three 1m2 throws are made within a few meters of each site center. Within each throw, all emergent macrophytes are counted (live and dead) and recorded. Submerged periphyton-associated aquatic vegetation are identified and recorded as a percentage of the total periphyton component. Macrophyte cover is recorded in percent cover, and average plant height is determined from three representative plants. Water depth is also recorded as an average of three depths.
Periphyton data collected from Northeast Shark Slough, Everglades National Park (FCE LTER) from September 2006 to September 2008
Periphyton assessments were conducted and recorded for each throw. Periphyton volumes, cover, type and composition were recorded, along with some general observations of the area. Periphyton samples were brought back for processing, and archived for soft algae, diatom, chlorophyll a, biomass and nutrient analysis.
Biogeochemical data collected from Northeast Shark River Slough, Everglades National Park, Florida, USA, September 2006 - April 2025
This project was established in 2006 to document the pattern of abundance of key ecological indicators (e.g., surface water, soil, floc, periphyton and sawgrass) across the NESRS landscape. A total of 30 sites were established and monitored in 2006, 2007 and 2008. After the completion of 1-mile bridge in 2012, additional 10 new sites were established to observe the ecological impact of 1-mile bridge (known as Bridge & Census sites). In 2015, additional 40 sites were established along eight transects (T1-T8, known as near canal sites) in ENP marshes starting at, and roughly perpendicular to the L-29 canal. The purpose of these sites was to monitor the potential effects of Modified Water Deliveries (MWD) operations on changing nutrient concentrations and ratios in key ecological compartments due to increased downstream discharges from the L-29 canal beneath the 1-mile and 2.6-mile bridges and culverts along Tamiami Trail. Data collection is complete.
Biogeochemical data collected in the eastern marl prairies of the Everglades (Florida, USA) before and after fire, between the years 2018 and 2021
The data included in this database were collected within a project funded by Everglades National Park (ENP). The project was aimed at understanding how fire, characterized by different intensities, differentially affects nutrient cycling in oligotrophic wetlands with distinct levels of phosphorus limitation. The data were collected in the eastern part of the Everglades, close to the boundary of ENP, in South Florida (Homestead). This part of ENP is characterized by marl soils, which are shallow (often less than 10 cm) and C-poor. The data were collected at two sites: one site was more oligotrophic (LP), while the other one had a certain degree of phosphorus enrichment (HP). The database includes date and location (i.e. site and plot) of each sampling event, surface water physio-chemistry, vegetation composition and structure, including dominant macrophyte estimated biomass, litter and root decomposition rates, and carbon, nitrogen, and phosphorus concentrations in the soil, flocculent detrital material, periphyton, sawgrass leaves and roots, and the water column. All these data were collected at different times between September 2018 and March 2021, before and after a prescribed fire that was carried out in February 2020 and which burned all the plots. Each row within the database identifies a unique combination of date and sampling plot.
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.
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).
AFLP and MS-AFLP data for Spartina alterniflora and Borrichia frutescens collected from three habitats (i.e. low, medium, and high salt) within five sites, respectively, on Sapelo Island, GA in May 2011
Using amplified fragment length polymorphism (AFLP) and methylation sensitive (MS)-AFLP we assessed genetic and epigenetic variation in two salt marsh perennials, Spartina alterniflora and Borrichia frutescens, in Sapelo Island, Georgia. We sampled Apex (A), Cabretta (C), Hunt Camp (H), Lighthouse (L), and Marsh Landing (M) for S. alterniflora, and C, H, L, M, and Shell Hammock for B. frutescens due to site specific differences in species among the sites. We tested the hypothesis that populatation structure at the habitat level would be due to epigenetic loci and not genetic. The presence and absence AFLP bands and MS-AFLP methylation respresents a genome-wide snapsnot of variation within individuals. We used hierarchical AMOVAs, permutational MANOVA, Bayesian clustering (genetic only), Mantel and partial Mantel tests, and generalized linear models to assess the spatial structure of genetic and epigenetic variation among our two study organisms across five sites for each organism. (Note: genetic and habitat distance tables were normalized for database compatibility. These data must be formatted as a square dissimilarity matrix for input to the code files.)
Meteorology and soil moisture data collected at multiple frequencies from the C-CALI NPP site automated monitoring stations: Jornada Basin LTER, 2013 - ongoing
This dataset contains summary data collected at the Jornada Basin LTER program's C-CALI NPP site weather station and associated soil substation at several temporal scales. Precipitation data are collected at 1-second frequency during rain events, air temperature and wind at 5-minute frequency, and all sensors are measured at 30-minute, hourly and daily frequencies. Observed values include average/maximum/minimum air temperature, relative humidity, and wind speed; average wind direction; total precipitation; soil moisture, temperature and conductivity. These are measured and calculated based on 1-second scan rate of all sensors located at an automated weather station, and a nearby soil substation, installed at the site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximately 2.5m. Soil sensors are installed at approximately 10, 20 and 30cm depths.
Meteorology and soil moisture data collected at multiple frequencies from the C-GRAV NPP site automated monitoring stations: Jornada Basin LTER, 2013 - ongoing
This dataset contains summary data collected at the Jornada Basin LTER program's C-GRAV NPP site weather station and associated soil substation at several temporal scales. Precipitation data are collected at 1-second frequency during rain events, air temperature and wind at 5-minute frequency, and all sensors are measured at 30-minute, hourly and daily frequencies. Observed values include average/maximum/minimum air temperature, relative humidity, and wind speed; average wind direction; total precipitation; soil moisture, temperature and conductivity. These are measured and calculated based on 1-second scan rate of all sensors located at an automated weather station, and a nearby soil substation, installed at the site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximately 2.5m. Soil sensors are installed at approximately 10, 20 and 30cm depths.
Meteorology and soil moisture data collected at multiple frequencies from the C-SAND NPP site automated monitoring stations: Jornada Basin LTER, 2013 - ongoing
This dataset contains summary data collected at the Jornada Basin LTER program's C-SAND NPP site weather station and associated soil substation at several temporal scales. Precipitation data are collected at 1-second frequency during rain events, air temperature and wind at 5-minute frequency, and all sensors are measured at 30-minute, hourly and daily frequencies. Observed values include average/maximum/minimum air temperature, relative humidity, and wind speed; average wind direction; total precipitation; average and total solar incoming and reflectance; average albedo; average net radiation; soil moisture, temperature and conductivity. These are measured and calculated based on 1-second scan rate of all sensors located at an automated weather station, and a nearby soil substation, installed at the site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, air temperature and relative humidity at approximately 2.5m, and solar at approximately 3m. Soil sensors are installed at approximately 10, 20 and 30cm depths.
Meteorology and soil moisture data collected at multiple frequencies from the G-BASN NPP site automated monitoring stations: Jornada Basin LTER, 2013 - ongoing
This dataset contains summary data collected at the Jornada Basin LTER program's G-BASN NPP site weather station and associated soil substation at several temporal scales. Precipitation data are collected at 1-second frequency during rain events, air temperature and wind at 5-minute frequency, and all sensors are measured at 30-minute, hourly and daily frequencies. Observed values include average/maximum/minimum air temperature, relative humidity, and wind speed; average wind direction; total precipitation; soil moisture, temperature and conductivity. These are measured and calculated based on 1-second scan rate of all sensors located at an automated weather station, and a nearby soil substation, installed at the site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximately 2.5m. Soil sensors are installed at approximately 10, 20 and 30cm depths.
Meteorology and soil moisture data collected at multiple frequencies from the G-IBPE NPP site automated monitoring stations: Jornada Basin LTER, 2013 - ongoing
This dataset contains summary data collected at the Jornada Basin LTER program's G-IBPE NPP site weather station and associated soil substation at several temporal scales. Precipitation data are collected at 1-second frequency during rain events, air temperature and wind at 5-minute frequency, and all sensors are measured at 30-minute, hourly and daily frequencies. Observed values include average/maximum/minimum air temperature, relative humidity, and wind speed; average wind direction; total precipitation; average and total solar incoming and reflectance; average albedo; average net radiation; soil moisture, temperature and conductivity. These are measured and calculated based on 1-second scan rate of all sensors located at an automated weather station, and a nearby soil substation, installed at the site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, air temperature and relative humidity at approximately 2.5m, and solar at approximately 3m. Soil sensors are installed at approximately 10, 20 and 30cm depths.
ScienceDex guides
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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.