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Species richness of vascular plants and bryophytes in nine grassland sites (Europe and California collected in 2013-2016)
We sampled vascular plants (VP) and bryophytes (non-vascular plant; NVP) 1×1 m experimental plots in nine sites belonging to the Nutrient Network. Three sites were in California, two in Finland and UK and one in Germany and Switzerland. The data were collected to compare the responses of NVPs and VPs to nutrient addition and grazing exclusion treatments. The NVP and VP cover sampling was conducted in March-August 2016, except for heron.uk and rook.uk, which had been sampled for VPs in 2013. NVPs were mostly identified to species, but in absence of necessary diagnostic characters (capsules, other reproductive organs, distinctive gametophytic features), some specimens were identified at morphospecies group, subgenus, or genus level. We calculated three plant diversity indices for NVPs, VPs and total (NVPs and VPs combined) in each plot. First, species richness (S) is the number of species per 1 m2 for NVPs and VPs. For plots having no NVPs, NVP richness is zero. Second, for plots having at least one NVP, we calculated Inverse Simpson’s index of diversity (referred to as species diversity), which is equivalent to the Probability of Interspecific Encounter or Effective Number of Species (ENSPIE). Third, we calculated Simpson’s evenness (E = ENSPIE/S; referred to as evenness), which was expected to reflect changes in species’ dominance. We also sampled aboveground plant biomass at peak biomass of vascular plants (in May- August, depending on local site level characteristics) by clipping at ground level and removing all aboveground vegetation (live and dead) from two 0.1 × 1 m strips, sorting the current year’s VP and NVP biomass from the previous year’s biomass (dead litter), drying the biomass to a constant mass at 60 °C, and weighing it to the nearest 0.01 g. Except for two sites (heron.uk and rook.uk), we also measured photosynthetically active radiation (PAR) at the ground surface and above grassland canopy at time of peak biomass and calculated the proportion of tra
Sacramento-San Joaquin Bay-Delta Continuous (15 minute) Water Quality Monitoring: South Delta Region, collected by the North Central Region Office, DWR, 1999 – ongoing
The Department of Water Resources (DWR) Water Quality Evaluation Section (WQES) provides technical expertise and program support for regulatory compliance, water operations, emergency response, and environmental restoration. Wireless telemetry is used to transmit real-time provisional data to the California Data Exchange Center (CDEC), making the data publicly available. The published dataset is quality controlled and quality assured providing detailed information at 15-minute intervals from 18 monitoring stations, using Xylem’s YSI EXO2 and YSI 6600 multiparameter sondes to document individual water quality measurements of multiple water quality parameters. The dataset informs operations for the California State Water Project and supports water quality monitoring required by Water Right Decision D-1641, the Delta Compliance Program, the South Delta Temporary Barriers and the South Delta Improvement Program. It is important to note that the start dates and subsequent equipment upgrades vary between stations and equipment leading to discrepancies in the dataset’s date ranges.
SJR Dolphin SCA: Degradation Scores, OL Length and Identifications of Otoliths Collected from Bottlenose Dolphin Stomachs
Otoliths were collected from stomach contents of stranded bottlenose dolphins (Tursiops erebennus) in the St. Johns River in Jacksonville, Florida. Otoliths were analyzed by a panel of 3 reviewers to determine the level of otolith degradation that occurred during digestive processes. Otoliths with scores ≤ 3 were measured. Otolith length measurements were used to estimate the size of most species by applying standard regression equations developed from fish species collected from a nearby water system, the Indian River Lagoon, and for one species, equations developed from violet gobies collected from the St. Johns River. These equations enabled estimation of the mass of each prey species in each dolphin’s stomach, then the calculation of their relative proportions of reconstructed mass across all stomachs. For otolith identification purposes, a panel of 4 reviewers assigned each otolith with a family-level and species-level identification. Each identification was given a confidence code ranging from 1 (no confidence) to 4 (certainty). When the average code for all reviewers was < 3, the otolith was considered unidentified. If two of the reviewers agreed with the “weight” reviewer and all gave scores ≥ 3, the score of the outlying reviewer was discarded. Identification was assigned when the average confidence code was ≥ 3. The minimum number of species per dolphin stomach was determined by counting the left and right otoliths for each species separately, using the higher count as the minimum prey number. Unidentified species were counted, and half of their sum was considered the minimum prey number. The frequency of occurrence (%FO, or proportion of stomachs in which a species was detected) and numerical proportion (%N, or proportion of a given species pooled across all stomach samples) of each prey species were then calculated.
Interagency Ecological Program: Fish catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2024.
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect 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. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. The 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. Only juvenile and adult fish catch with associated water quality are presented in this dataset. The rotary screw trap sampling objectives are to: (1) examine species abundance and life stage of juvenile outmigrants and resident small-bodied fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, and (3) examine the effect of physical and environmental conditions on these patterns. The fyke trap sampling objectives are to: (1) examine abundance of migrating and resident adult fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, especially with regard to anadromous species, (3) examine the effect of physical and environmental conditions on these patterns, and (4) provide data on the timing and duration of species captured in the Yolo Bypass for comparison to those captured in other Sacramento Valley tributaries. The beach seine surveys are conducted in the Yolo Bypass’s perennial channel (Toe Drain), inundated floodplain, disconnected inundated ponds, and perennial ponds. The objectives o
Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2025
The United States Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook Salmon Oncorhynchus tshawytscha and other fish species within the San Francisco Estuary (Estuary) since 1976 using a combination of surface trawls and beach seines. Since 2000, three trawl sites and 58 beach seine sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin Rivers. As part of the Interagency Ecological Program (IEP) that manages the Estuary, the DJFMP has tracked the relative abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon of all races as they outmigrate through the Sacramento-San Joaquin Delta for over four decades. The data that DJFMP collected has been used not only to help inform the management of Chinook Salmon, but also to monitor the status of native species of interest such as the previously listed Sacramento Splittail Pogonichthys macrolepidotus and invasive species such as Mississippi Silverside Menidia audens and Largemouth Bass Micropterus salmoides. DATA CORRECTION/UPDATE: Previous data versions 244.6, 244.7, and 244.8 contained an error and resulted in duplicated records of hatchery Chinook Salmon in the datasets. These datasets were removed from the data repository and the error was corrected in version 244.9 and after. DNA Data: Full more details of the DNA methods and results for juvenile Chinook salmon included in this dataset, please check out Blankenship, S.M., J. Israel, E. Buttermore, and K. Reece. 2021. Knights Landing, California Department of Fish and Wildlife, Genetic Determination of Population of Origin 2017 through 2019 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/85fbc988c0b1362e84c318e69c7a939e. For more information on the Delta Juvenile Fish Monitoring Program: https://www.fws.gov/project/delta-juvenile-fish-monitoring-program
Zooplankton density for all samples collected from Toolik Lake and lakes near the Toolik Field Station, Arctic LTER 2003 - 2017 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-arc/10272/5. The abstract below was extracted from the Level 0 data package and is included for context: Zooplankton density,were taken with a 30 cm diameter plankton net with 156 um mesh plankton netting, for all samples collected from Toolik Lake and lakes near the Toolik Field Station, Arctic LTER from 2003 - 2017. The Arctic is one of the most rapidly warming regions on Earth. Responses to this warming involve acceleration of processes common to other ecosystems around the world (e.g., shifts in plant community composition) and changes to processes unique to the Arctic (e.g., carbon loss from permafrost thaw). The objectives of the Arctic Long-Term Ecological Research (LTER) Project for 2017-2023 are to use the concepts of biogeochemical and community “openness” and “connectivity” to understand the responses of arctic terrestrial and freshwater ecosystems to climate change and disturbance. These objectives will be met through continued long-term monitoring of changes in undisturbed terrestrial, stream, and lake ecosystems in the vicinity of Toolik Lake, Alaska, observations of the recovery of these ecosystems from natural and imposed disturbances, maintenance of existing long-term experiments, and initiation of new experimental manipulations. Based on these data, carbon and nutrient budgets and indices of species composition will be compiled for each component of the arctic landscape to compare the biogeochemistry and community dynamics of each ecosystem in relation to their responses to climate change and disturbance and to the propagation of those responses across the landscape.
Interagency Ecological Program: Zooplankton catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2018
Largely supported by the Interagency Ecological Program (IEP), the California Department of Water Resources (DWR) has operated a fisheries and invertebrate monitoring program in the Yolo Bypass since 1998. The main objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to collect baseline data on lower trophic levels (phytoplankton, zooplankton and insect drift), juvenile and adult fish, hydrology, and water quality parameters. As the Yolo Bypass has been identified as a high restoration priority by numerous regulatory agencies, these baseline data are critical for evaluating success of future restoration projects. In addition, the data have already served to increase our understanding of the role of the Yolo Bypass in the life history of native fishes, and its ecological function in the San Francisco Estuary. Zooplankton are an important component in the diet of larval, juvenile, and small adult fishes within the San Francisco Estuary, including Delta Smelt, juvenile Chinook Salmon, Striped Bass, and Sacramento Splittail. The YBFMP collects zooplankton year-round from two sites. Since 2011, samples have been collected biweekly (every other week) to weekly (during floodplain inundation) using 150- and 50- micrometer mesh plankton nets. Zooplankton are identified and enumerated by contractors (currently BSA Environmental Services). The goals of the zooplankton monitoring program are to compare the seasonal variation in species densities and trends between (1) the Sacramento River channel, and (2) the Yolo Bypass, the river’s seasonal floodplain. Data on zooplankton catch and associated water quality parameters are presented in this dataset.
Interagency Ecological Program: Drift invertebrate and ichthyoplankton catch and water quality from the Sacramento River channel, and Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2022
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect 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. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. Aquatic and terrestrial insects are an important component in the diet of juvenile and adult fishes within the San Francisco Estuary, including two important native fishes: juvenile Chinook Salmon and Sacramento Splittail. The YBFMP collects drift invertebrates year-round from two sites. Currently, samples are collected biweekly (every other week) to weekly (during floodplain inundation) using a rectangular aquatic drift net that sits at the surface of the water. Invertebrates are identified and enumerated by contractors (currently EcoAnalysts, Inc.). The goals of the monitoring program are to compare the seasonal variations in densities and species trends of aquatic and terrestrial insects/non-insects within the Sacramento River channel and the Yolo Bypass, the river’s seasonal floodplain. Drift invertebrate Key findings to date include: (1) Chinook Salmon sampled in the floodplain had diets comprised of 90% Dipterans and zooplankton, with Chironomidae being the dominant Diptera family (Sommer et al., 2001), (2) The floodplain of the Yolo Bypass contains significantly higher densities of Diptera (Diptera densities being positively associated with flow) and terrestrial invertebrates than the adjacent Sacramento River (Sommer et al. 2001b: Sommer
Interagency Ecological Program and US Fish and Wildlife Service: Juvenile/Larval Fish and Zooplankton collections at Liberty Island, California 2002-2005 & 2013-2019
The U.S. Fish and Wildlife Service (USFWS) Lodi Fish and Wildlife Office (LFWO) Delta Juvenile Fish Monitoring Program (DJFMP) has intermittently sampled Liberty Island with various equipment since 2002. Liberty Island was a reclaimed agricultural island until it flooded in 1997-1998 and we subsequently left to passively restore as a tidally influenced wetland. Larval trawls and beach were the only sampling methods used during both early (2002-2005) and late (2009-2019) sampling periods. The main purpose of the sampling was to gather information about fish presence and abundance in Liberty Island during the passive restoration, with an emphasis on reproductive and early life-stages of native species. Larval trawls, or tow nets, were used to catch larval fish in 2004-2005 and again from 2013-2019. Zooplankton nets were used 2013-2019. Water quality measurements were collected alongside each tow.
Vegetation indices calculated from reflectance spectra collected at LTER plots at Toolik Lake, Alaska during the 2007-2019 growing seasons.
Vegetation indices calculated from reflectance spectra collected at Arctic LTER experimental plots at Toolik Lake, Alaska during the 2007-2019 growing seasons. Long term experimental plots span several different vegetation types: Heath (HTH89), Moist Acidic Tussock (MAT89 and Low Fert), Moist Non-Acidic Tussock (MNAT), Non-Acidic Non-Tussock (NANT), Shrub (SHB), and Wet Sedge (WSG). Plots are differentiated by their experimental treatment and are located in replicate blocks.Canopy reflectance is measured by hand-held spectrophotometer and several indices of interest (NDVI, EVI, EVI2, PRI, WBI, and Chlorophyll index) are calculated.
Mass per tiller, nitrogen concentration, stable isotope ratios for carbon and nitrogen from the 1980-82 Eriophorum vaginatum reciprocal transplant experiment along a latitudinal gradient in interior Alaska collected in July, 2011
In 1980-1982, six transplant gardens were established along a latitudinal gradient in interior Alaska from Eagle Creek, AK in the south to Prudhoe Bay, AK in the north. Three sites, Toolik Lake (TL), Sagwon (SAG), and Prudhoe Bay (PB) are north of the continental divide and the remaining three, Eagle Creek (EC), No Name Creek (NN), and Coldfoot (CF), are south of the continental divide. Each garden consisted of 10 individual Eriophorum vaginatum tussocks transplanted back to their home-site, as well as 10 individuals from each of the other transplant sites. The gardens were harvested in 2011. Important variables are garden name, source population, mass per tiller, nitrogen concentration, and stable isotope ratios for Carbon and Nitrogen.
Toolik Lake Inlet discharge data collected during summers of 2010 to 2018, Arctic LTER, Toolik Research Station, Alaska.
Stream discharge, temperature, and conductivity of Toolik Lake Inlet stream for 2010 - 2018 study season. Water level was recorded with a Stevens PGIII Pulse Generator and Conductivity (EC) and Temperature measured with a Campbell Scientific Model 247 Conductivity and Temperature probe.
Soil temperature data collected from the Arctic LTER wet sedge experimental site Toolik Field Station North Slope, Alaska from 1994 to 2020
Soil temperature data collected every 4 hours from a wet sedge site at the Arctic Tundra LTER site at Toolik Lake. Temperatures are measured every 3 minutes and averaged every 4 hours in control, nitrogen alone, phosphorus alone, nitrogen and phosphorus, and greenhouse experimental plots soil temperatures.
Meteorological data collected on Lake E5 during the ice free season since 2000 to present, Arctic LTER, Toolik Research Station, Alaska.
Yearly file describing the metological data on Lake E5 (Lake E5 Climate station) near the Toolik Field Research Station (68 38'N, 149 36'W). Measurements include air temperature, relative humidity, wind direction, and wind speed..
Presence/absence of new snow-fall scored from time-lapse photography collected near Toolik Field Station, Alaska, summers 2012-2016
This data set describes the presence/absence of new snowfall approximated daily using time -lapse photography images near Toolik Field Station during summers 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). Additional cameras funded by other grants were also used for scoring including multiple Toolik EDC timelapse images taken at Toolik, Atigun Ridge, and Imnavait. Additional data were scored from time lapse photography taken by the Deegan and Urban labs (Office of Polar Programs #0902153 and #1417664). All data are associated with publication DOI: 10.1111/jav.01712.
Vegetation Data Collected with Point Frame for 83 Locations of 6-163 Years Old Black Spruce, Alaska Paper Birch, and Aspen Stands Across Interior Alaska. Sampled in 2008-2010 and 2013-2015.
This dataset contains point frame data for vegetation less than 1.3 m, including vascular plants, bryophytes, lichens, leaf litter and bare ground, as well as species codes used, as described in Jean et al. 2017 Canadian Journal of Forest Research. Samples of all encountered unknown species were collected for identification in the lab. Bryophyte nomenclature followed Anderson et al. (1990).
Overwintering Fires from 2009-2010 Burns near Fairbanks, Alaska: Post-fire Seedling Recruitment Collected 2023
This dataset contains data from adjacent overwintering and single-season burn sites. For the overwintering fires, we targeted locations that had burned in the summers of 2009, smouldered through the winter months, and reignited in 2010. Adjacent to these overwintering sites, we identified single-season burn sites from within portions of the 2009 fires that were unaffected by overwintering. A total of seven overwintering fire sites and four single-season fire sites were sampled. Within each site, three plots were established. Data inlcudes within plot measurments of post-fire seedling composition and density, residual SOL, burn depth estimated by black spruce adventitious roots, thaw depth, and pre-fire tree species composition and estimates of combustion. This is one of three packages from this project; this one contains the seedling recruitment data.
Overwintering Fires from 2009-2010 Burns near Fairbanks, Alaska: Residual Soil Organic Layer Depth, Burn Depth and Thaw Depth Collected 2023
This dataset contains data from adjacent overwintering and single-season burn sites. For the overwintering fires, we targeted locations that had burned in the summers of 2009, smouldered through the winter months, and reignited in 2010. Adjacent to these overwintering sites, we identified single-season burn sites from within portions of the 2009 fires that were unaffected by overwintering. A total of seven overwintering fire sites and four single-season fire sites were sampled. Within each site, three plots were established. Data inlcudes within plot measurments of post-fire seedling composition and density, residual SOL, burn depth estimated by black spruce adventitious roots, thaw depth, and pre-fire tree species composition and estimates of combustion. This is one of three packages from this project; this one contains the soils data.
Overwintering Fires from 2009-2010 Burns near Fairbanks, Alaska: Pre-fire Tree Species Density and Combustion Collected 2023
This dataset contains data from adjacent overwintering and single-season burn sites. For the overwintering fires, we targeted locations that had burned in the summers of 2009, smouldered through the winter months, and reignited in 2010. Adjacent to these overwintering sites, we identified single-season burn sites from within portions of the 2009 fires that were unaffected by overwintering. A total of seven overwintering fire sites and four single-season fire sites were sampled. Data inlcudes within plot measurments of post-fire seedling composition and density, residual SOL, burn depth estimated by black spruce adventitious roots, thaw depth, and pre-fire tree species composition and estimates of combustion. This is one of three packages from this project; this one contains the pre-fire tree species density and combustion data.
Experimental Studies of Pollination of Viburnum edule (highbush cranberry) Collected in the Spring of 2020 and 2021 at Interior Alaska Sites around Fairbanks, Alaska
This dataset contains the results of experimental studies of pollination of Viburnum edule (highbush cranberry) in spring of 2020 and 2021. It compares pollinator visitation rates, pollen deposition, and the composition of the pollinator community between inflorescences exposed at the very start of the flowering period and at peak flowering and between the two years . It also contains the results of a pollinator exclusion experiment conducted in spring of 2020.
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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.