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openCC0Jan 2025View details →

Central Valley Project, Genetic Determination of Population of Origin 2011-2024

Central Valley Chinook Salmon populations differ in their Endangered Species Act listing status. It is often difficult to distinguish individuals from the different Evolutionarily Significant Units. As such, many of the salmon monitoring and evaluation efforts in the Central Valley and San Francisco Bay-Delta are hampered by uncertainty about population (stock) identification and proportional effects of management actions (Dekar et al. 2013; IEP 2019). Studies have identified that the current identification method (length-at-date models) of juvenile Chinook salmon (Fisher 1992) captured in the watershed vary in their accuracy, particularly for spring-run (NMFS 2013; Harvey et al. 2014; Merz et al. 2014). The inaccuracy of the size-based methods is likely due to differences in fish distribution during early rearing, habitat-specific growth rates, and inter-annual variability in temperatures and food availability that lead to overlap in size ranges among stocks. The primary objective of this project was the genetic classification (to race; Evolutionary Significant Unit) of Chinook Salmon captured from State Water Project and Central Valley Project fish protection facilities and Interagency Ecological Program monitoring programs. The population-of-origin was determined for sampled fish by comparing their genotypes to reference genetic baselines. Genetic methods, having less statistical uncertainty that size-based models for population identification, were intended to directly target (and reduce) one source of uncertainty in the estimation of loss (take) from water diversions (operations) and develop the information necessary for understanding stock-specific distribution, habitat utilization, abundance, and life history variation. This project supports recommendations from the Interagency Ecological Program’s Salmon and Sturgeon Assessment of Indicators by Life Stage and Interagency Ecological Program Science Agenda efforts to improve Central Valley salmonid monitoring

Minnesota Department of Natural Resources Yellow Perch and Bluegill Diet Study, Lower Pool 4 Mississippi River, 2018-2019

To assess potential dietary overlap and predation between bluegill and yellow perch, we examined stomach content of both species in three backwater contiguous lakes of Lower Pool 4 in the Mississippi River from May 2018 through January 2019. In this area, bluegill have been common for decades, but yellow perch only became abundant following an ecological shift to a clear-water, macrophyte dominated state that occurred from 2007 - 2007. We used daytime electrofishing to collect fish during open-water sampling (spring, summer, and fall) and ice angling during ice-covered sampling (winter). The dataset documents the diet content of one hundred and eighty-nine yellow perch and sixty-one bluegill. Stomach contents were extracted via gastric lavage in the spring, summer, and fall and via stomach removal in the winter. All prey items were categorized to lowest identifiable taxonomic level and quantified via volumetric displacement.

US_UMB and US_UMd Ameriflux towers biometric plot data at the University of Michigan Biological Station, Pellston, MI (1997 to 2024)

These are the annual leaf litterfall carbon fluxes and average soil respiration measurements for the two flux towers (reference, aka 'AmeriFlux' and treatment, aka 'FASET') at UMBS.

Microclimate temperature effects propagate across scales in forest ecosystems, Berchtesgaden National Park, Bavaria, Germany

Context: Forest canopies shape subcanopy environments, affecting biodiversity and ecosystem processes. Empirical forest microclimate studies are often restricted to local scales and short-term effects, but forest dynamics unfold at landscape scales and over long time periods. Objectives: We developed the first explicit and dynamic implementation of microclimate temperature buffering in a forest landscape model and investigated effects on simulated forest dynamics and outcomes. Methods: We adapted the individual-based forest landscape and disturbance model iLand to use microclimate temperature for three processes [decomposition, bark beetle (Ips typographus L.) development, and tree seedling establishment]. We simulated forest dynamics with or without microclimate temperature buffering in a temperate European mountain landscape under historical climate and disturbance conditions.

openCC0Aug 2025View details →

Juvenile Salmonid Emigration Monitoring in the Stanislaus River at Oakdale, California, 1996-2023

The operation of the rotary screw trap on the lower Stanislaus River at Oakdale Recreation Area is one of the longest-running datasets (1996-2023) in the Central Valley for juvenile salmonids. The primary objectives of the study are to collect data that can be used to estimate the passage of juvenile fall-run Chinook Salmon (Oncorhynchus tshawytscha) and to quantify the raw catch of Oncorhynchus mykiss. Secondary objectives of the trapping operations focus on collecting biological data on juvenile salmonids and gathering environmental data that will be used to develop models that correlate environmental parameters with salmonid size, temporal presence, abundance, and production.

Root Biomass, Fine Root Production, Soil Mass, and Soil pH in Limed and Control Plots at the Woods Lake Watershed, Adirondack Park, NY, USA, 2021-2022

In 1989, 6.89 Mg/ha of pelletized lime (CaCO3) was applied by helicopter to two subcatchments at the Woods Lake Watershed in Adirondack Park, New York, USA to ameliorate ecosystem acidification. Two unlimed (control) subcatchments were paired with limed subcatchments. In the same year, 99 permanent plots (20 m x 20 m) were established. Between 2008 and 2010, tree inventory and soil physicochemical measurements were made in five plots in each of the four subcatchments (20 plots total). This dataset contains soil physicochemical properties (dry mass, depth, and pH); root biomass (<1 mm, 1-2 mm, and >2 mm diameter); and annual fine root production (<1 mm and 1-2 mm) measurements made between 2021 and 2022 in 19 of these same plots (5 plots per control subcatchment and 4 or 5 plots per limed subcatchment). Data include measurements for all properties for Oe, Oa, and 0-10 cm mineral soil samples collected from 5 locations within each plot.

CO2 Flux and Temperature Data for Estimating Thermal Acclimation in Ecosystem Respiration

We have compiled an extensive dataset of long-term, hourly CO2 flux measurements from 93 global eddy covariance sites to estimate the thermal response strength in nighttime ecosystem respiration. Flux data was sourced from AmeriFlux (https://ameriflux.lbl.gov/), FluxNet (https://fluxnet.org/), and ICOS (https://www.icos-cp.eu/). The processed data product encompasses five categories. (1) Long-term, directly measured, Ustar-filtered, hourly or subhourly nighttime ecosystem respiration, along with corresponding air temperature, soil temperature, and soil water content at the 93 sites. (2) Long-term gap-filled data, including hourly or subhourly net ecosystem exchange, air temperature, and soil temperature at these sites. (3) Annual topsoil (< 0.1 m) temperature and nighttime ecosystem respiration curves during the growing season, designed for calculating thermal response strength. (4) Estimated thermal response strength across these sites, detailed with geographic, climatic, soil, and vegetation conditions for each site. (5) An R script to calculate thermal response strength using the data product (3).

Root fungi isolated from common Louisiana marsh plants 2017-18.

Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here we collected data to investigate environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three-four dominant plant species from each of three sites of varying salinity. We provide data on abundance and taxonomy of the isolated fungal taxa as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD).

openCC (other)Feb 2026View details →

Weight, sex, age, beam diameter, antler points and teat length for harvested deer from 1984-2025 in Black Rock Forest, Cornwall, NY.

Data from white-tailed deer harvested within Black Rock Forest, Cornwall, New York are collected annually. Trained staff measure mass, antler beam diameter, and teat length (since 2010), estimate age via dentition, count antler points, and assess sex on all field-dressed deer. Heart girth, measured as chest circumference, was recorded from 1984 to 1998.

openCC (other)Jul 2021View details →

SBC LTER: Reef: Kelp Forest Community Dynamics: Fish abundance (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-sbc/17/35. The abstract below was extracted from the Level 0 data package and is included for context: These data describe the abundance and size of fish species as part of SBCLTER's kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area. The two tables in this data package include: 1) The annual benthic fish community survey which was conducted on 11 reefs once a year around late July or early August; and 2) The monthly fish survey which was conducted once a month at a subset of the sites (3 of the annual sites) The time period of data collection for the annual benthic fish community survey varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The monthly fish survey at ABUR (Transect 1, 2, and 3), AQUE (Transect1), and MOHK (Transect 1) in 2002. The Transect 2 and 3 at ABUR were discontinued in June 2006. See Method

openCC0Feb 2025View details →

Code for Random Forest models that predict pharmaceutical and water chemistry measurements in Baltimore Ecosystem Study streams

This file contains code to model the relationship between the water chemistry measurements and discharge measured as part of BES routine sampling and the pharmaceuticals measured in WY 2018. We use Random Forest models to predict 1) total (i.e., summed) concentration of the pharmaceuticals for which we screened, 2) total nutrient concentrations (TN & TP), 3) whether or not the antibiotic trimethoprim was detected in a given sample, and 4) whether or not nitrate and TP were above or below environmentally-relevant threshold concentrations. We also use RF models to predict N and P concentrations over a longer period, in order to compare models for nutrients to pharma. Code and analyses here rely on data processed in the file "BESPharma_WY2018.Rmd", published on EDI (doi:10.6073/pasta/610cb67fcbc8982c2af8ed946dce8ea5) and BES water chemistry data published on EDI (doi:10.6073/pasta/ce7f30e6013e003bfe28c5fd7d4aed23 )

Field Evidence of Carbon and Nitrogen Stabilization through Mineral Associated Organic Matter Formation in Coastal Wetland Soils from Apalachicola, Florida, collected in June, 2022.

This data set was used to observe the role of Mineral Associated Organic Matter Formation (MAOM) on biogeochemical soil properties in three coastal wetlands in Apalachicola, Florida. One wetland was restored using beneficial dredged sediment, increasing the soil's inorganic matter content. Soil samples were collected in June 2022 from this wetland and two nearby reference wetlands: one with high organic matter and the other with higher inorganic matter content. The samples were analyzed at the University of Central Florida for biogeochemical properties to determine which properties were most related to MAOM pools.

openCC0Feb 2025View details →

Introductory Motus Prioritization Tool Data (Open first)

Addressing survival and movement of priority migratory avian species of concern along the Pacific Flyway is paramount for their conservation. Yet, the migratory life stage is understudied in many avian species. The Motus radiotelemetry receiver network is an established system for tracking survival and movement of avian species. This network is an international collaborative that successfully identifies stopover site duration, connected migratory routes, post-fledging dispersal and survival, and adult survival and fidelity on a landscape-scale; parameters that cannot be easily estimated using non-tagged birds. While the Motus network is highly connected in eastern North America, the western part of the continent is lagging in coverage and connectivity, limiting the ability to obtain sample sizes large enough to robustly model demographic parameters from tagged birds. Thus, the expansion of the Motus network is a high priority for Pacific Flyway State Agencies. To date, no method exists for determining priority locations for new Motus receiving stations. With collaborations from States and the Canadian Province of British Columbia, we used eBird citizen scientist data to prioritize strategic locations for new Motus receiving stations throughout the Pacific Flyway. We model priority species’ co-occupancy of varying abundance states (i.e., absent, present, abundant, abundant in multiple weeks) with spatially varying Landsat (red and near infrared), water, land cover types, and weather covariates while accounting for variable detection with temporally varying survey effort covariates. Using occupancy model predictions, we identify high-use areas of the Pacific Flyway for establishing new Motus receiving towers that have high probabilities of intercepting high presence and /or abundance of multiple species of interest in a series of predictive occupancy maps. This package contains required files to recreate the data analysis, print out maps based on predictions from the

Great Bay Estuary, NH/ME, Box Model Water Chemistry, Flow, Precipitation, and Seagrass Coverage Data, 2008 - 2023.

This data repository contains compiled surface water (tributary and estuarine), wet deposition, and wastewater effluent chemistry, along with discharge, precipitation totals, and monthly effluent flows necessary for the completion of solute budgets for Great Bay, a subregion of Great Bay Estuary, NH/ME, USA. These datasets are part of on-going monitoring programs in the Great Bay Estuary and Lamprey River Hydrological Observatory. A subset of the monitoring data for the 2008 to 2023 period was compiled. The tributary and estuarine monitoring data were requested from the NH Department of Environmental Services Environmental Monitoring Database as part of the Tidal Tributary and Estuary Water Quality Monitoring Programs. The wet deposition chemistry record is maintained as part of the Lamprey River Hydrologic Observatory. Wastewater effluent chemistry was downloaded from the EPA's Enforcement and Compliance History Online Database. The annual (1996 - 2023) seagrass coverage dataset for Great Bay Estuary reflects coverage of Zostera marina seagrass only and was compiled from annual monitoring reports. Mean daily instantaneous discharge data for the three tidal tributaries used in the load calculations are available from the USGS National Water Information System. Hourly precipitation volume data for the Durham, NH SSW station are available from the NCDC U.S. Climate Reference Network, with minor hourly gaps filled using the University of New Hampshire Durham weather station (https://www.weather.unh.edu).

Natural Regeneration of Puerto Rican Tropical Dry Forest Sites with Limited Burn History, Guánica Forest, 2012

This dataset documents the natural regeneration of tropical dry forest sites with limited burn history in Guánica Forest, Puerto Rico, following fire disturbance. Featuring a 29-year chronosequence, the dataset encompasses both short-term (2–5 months) and long-term (2–29 years) recovery, alongside mature forest control sites (including forest sites containing native grass). Data collection was conducted between May and August 2012 and focuses on woody tree species only. The dataset includes tree census data from seven sites (chrono_census.csv), recording species identity, stem diameter, aboveground biomass destruction, and resprouting dynamics. Additional data include species mean trait values, such as relative bark thickness and specific leaf area, to examine relationships with post-fire resprouting (chrono_traits.csv), and a species abundance matrix for evaluating community composition shifts over time (chrono_ndmsmatrix.csv). Field data were collected from circular 100 m² plots randomly placed at each site, with all woody plants tagged and identified. Stem diameters (≥1 cm) were measured at breast height (DBH) or ground height (DGH) in new-burn sites. Tree mortality was assessed, and aboveground biomass loss (0–100%) was estimated in new-burn sites. Resprouting was also quantified in short-term regeneration sites in mid-August 2012. In long-term sites, tree height was measured for the five tallest individuals. The dataset is relevant for researchers investigating tropical dry forest dynamics, fire ecology, and regeneration processes in Caribbean forest ecosystems. The dataset is complete and not ongoing.

Baltimore forest patch point-sample overstory and understory vegetation, 2018-2020

Urban forest patches, including woodland interiors and bounding edge habitat, result from secondary succession and fragmentation of more extensive forested landscapes in the eastern USA. Management regimes, surrounding land use, and successional processes lead to distinct environments and contribute to local and regional heterogeneity. However, many woodlands are degraded due to frequent disturbance, aggressive exotic species, and heavy browsing, which stress canopies, reduce regeneration, and may reduce ecosystem services. Effective management requires rapid, repeatable assessment of forest composition, structure, and condition at the scale of local decision-making. We present and apply a protocol for characterizing urban woodlands that generates new insight into the status of urban woodlands and baseline data for change detection over time. Samples of overstory composition, ground cover, surface soil measurements, and the Schumacher Vine Encroachment Index were collected at 845 points across each of 47 patches across Baltimore, Maryland. Simple citywide summaries allowed characterization of Baltimore’s urban overstories as overwhelmingly native, though dominated by a range of successional conditions. By contrast, we found that ground layers were predominantly exotic, with abundant invasives or ruderal native species benefitting from disturbed conditions. Seven overstory types were distinguished, the majority under threat from aggressive vines. Most soils showed little evidence of compaction, but variable organic content. Distributed data allowed crosspatch comparison as well as within-patch analyses along edge-to-interior gradients. Species diversity, nativity, and overstory basal area all increased towards woodland interiors, whereas soil compaction and vine encroachment decreased. Structural and compositional shifts in both overstory and ground layer species revealed indicators of edge (15.2-18.7 m) and interior (> 41.5 m) conditions, as well as evidence of tran

Beaver Dams in Madison and Oneida Counties, New York State, 1994-2022

This point dataset comprises georeferenced (NAD 1983 Zone 18N) digital markers of beaver dam locations in the Counties of Madison and Oneida in New York State in the years 1994, 2003, 2013, and 2022, as determined manually and retroactively through observation of true-color (rgb) composite aerial imagery from those years. The New York State Orthoimagery Database supplied the relevant imagery, and the years were chosen according to the availability of imagery for both counties at the time of data collection. The approximately 40-inch resolution photographs from 1994 were taken as part of the United States Geological Survey’s National Aerial Photography Program, whereas the 6- to 12-inch resolution images from the subsequent years were taken as part of New York’s GIS Coordinate Program. Each point represents a unique beaver dam determined to be present in one or more of the aforementioned years from such land feature characteristics as curvilinearity, perpendicular orientation to streams, proximity to apparent beaver lodges, and other distinguishing contextual clues. The attribute fields to the point data include the smallest unit of watershed in which the dam in question lies or once lay, the approximate location of the dam in terms of a named geographic feature, and one field for each year with a code indicating whether the dam was found to be present that year (1-yes, 0-no). This inventory has been used thus far in an investigation of the changes in dam abundance and distribution over the past three decades.

Soil respiration rates, biogeochemical pools, and mineral-associated organic matter from high organic matter and high mineral content coastal wetland soils in Apalachicola, Florida, 2022

This data set was used to observe how the application of dredged sediment would impact soil respirations rates, biogeochemical pools, mineral associated organic matter of coastal wetland soils from Apalachicola, Florida. To achieve this, a combination of intact core and bottle incubations were used, comparing a high organic matter coastal wetland soil to a high mineral content wetland soil which were collected in June, 2022. All laboratory analysis was conducted at the University of Central Florida in Orlando, Florida.

Cardiorespiratory metrics of cobia during and following a Ucrit trial upon a 3 wk exposure to either ambient or elevated pCO2

This study examined cardiac and swimming performance during a maximum sustained swimming trial (Ucrit) of cobia (Rachycentron canadum) following a three-week exposure to either elevated (~1,600 µAtm) or ambient (~500 µAtm) pCO₂. This dataset encompasses cardiac variables (stroke volume, heart rate, and cardiac output) during swimming and recovery from a Ucrit trial, hematological variables (hemoglobin, hematocrit, mean corpuscular hemoglobin concentration) following the swimming test and hour long recovery, oxygen consumption variables (MO₂ min, MO₂ max, aerobic scope, and factorial aerobic scope) during and following the swimming test.

Water temperature in the hidden, subglacial lake at Uruguay Island, Antarctic Peninsula region, 2020-2021, and additional data sets.

The dataset contains temperature measurements in a small subglicer (hidden) lake of Antarctic Peninsula region at several levels of depth. The measurements cover almost a full year and provide an understanding of the temperature and hydrological regime of the water body. Weather measurement data and statistics is provided additionally.