Find research datasets worth reusing

openCC (other)Dec 2021View details →

Knights Landing, California Department of Fish and Wildlife, Genetic Determination of Population of Origin 2017 through 2019

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

openCC (other)Feb 2022View details →

Cyanobacteria abundance, cyanotoxin concentration, and water quality data for the upper San Francisco Estuary, California, USA: 2014-2019

The goal of these measurements was to quantify Microcystis abundance and microcystin concentration and associated water quality conditions during summer blooms in the upper San Francisco Estuary in California, USA. Blooms of harmful algae are a major ecological concern in the area because harmful algae produce toxins and other metabolites, which deteriorate water quality and negatively impact the aquatic ecosystem. Our research team collected biological, physical, and chemical data at 2-week to 4-week intervals during the summer and fall from 2014 through 2019. Data included surface measurements of Microcystis volume (area-based diameter) by microscopy (flowCAM digital imaging flow cytometry) and subsurface (1 m depth) measurements of Microcystis, Aphanizomenon and Dolichospermum cell abundance measured by quantitative PCR, cyanotoxin concentration (total microcystins, anatoxin a and saxitoxin) measured by protein phosphatase inhibition assay or enzyme linked immunosorbent assay, and a suite of water quality parameters (water temperature, dissolved oxygen, nutrient concentration, water transparency, specific conductance, turbidity, pH, and chlorophyll a concentration). Details for the field sampling and analytical methods are available in Lehman et al. (2017). We also performed shotgun metagenomic analyses to investigate biodiversity of cyanobacteria and other aquatic microorganisms and all the DNA sequencing data are publicity available (www.ncbi.nlm.nih. gov/; BioProject ID: PRJNA434758, Kurobe et al. 2018, Lehman et al. 2021). During the study, we experienced critically dry (2014 and 2015), below normal (2016 and 2018), and wet years (2017 and 2019), therefore data obtained in this study provided a unique opportunity to assess impacts of extreme conditions on the aquatic ecosystem (Kurobe et al. 2018, Lehman et al. 2020).

openCC (other)Apr 2023View details →

Submersed Aquatic Vegetation community multi-year data from the Sacramento - San Joaquin Delta in California

Since 2007, field data have been collected in the Sacramento - San Joaquin Delta in northern California for the purpose of training and validating invasive species maps derived from remote sensing imagery over the Delta. The field crew collected submersed aquatic vegetation (SAV) species location data. For each point they noted attributes such as species name(s), location, cover estimates, and patch size. In addition, a thatching rake tethered to a rope was thrown off the side of the boat and pulled back out of the water; Secchi depth was measured using a Secchi disk and depth to the SAV mat was estimated by the field crew. Points were collected in patches larger than 9 square meters (3 m x 3 m). Point locations were measured using high precision (sub-meter accuracy) Trimble DGPS units (Trimble Navigation Limited, Sunnyvale, California) with Wide Area Augmentation System (WAAS) differential correction. All data points were exported as ArcGIS shapefiles and projected to UTM Zone 10N, Datum WGS-84 however this dataset includes the Latitude and Longitude of each point in decimal degrees. The spatial and attribute data quality was checked by examining photos of the data points and confirming the identify of the documented species.

openCC (other)Apr 2023View details →

Invasion dynamics of quagga mussels within a Southern California reservoir and its spatially intermittent watershed

Since its discovery in Lake Mead, Nevada in 2007, the invasive quagga mussel (Dreissena rostriformis bugensis) spread throughout the lower Colorado River drainage and into connected Southern California water systems. In December 2013, quagga mussels were found in Lake Piru, California, a reservoir with no connection to the Colorado River drainage. An initial “boom” period occurred in the first year after colonization. High densities and settlement rates continued for three years while lake water levels were low and relatively stable, despite periodic removals of mussels from lake infrastructure. Mussels were initially restricted to hard substrates but were regularly found on soft sediments within two years of colonization. Storms in 2017 dramatically increased the lake level and deposited substantial sediment, which eliminated mussels on soft sediments and reduced the overall mussel population. Reproduction and juvenile settlement rebounded within 6 months, despite the low population of adult mussels in the lake. Environmental conditions, particularly fill status and water temperature, rather than adult density, appear to be the primary driver of veliger abundance in this system, while recruitment was primarily explained by veliger abundance. Elevated water releases from the reservoir increased the flux of veligers downstream and led to mussel recruitment >15 km downstream. Sustained establishment of quagga mussels downstream has not occurred in the Santa Clara River and seems unlikely due to the unstable habitat conditions. However, periodic downstream colonization increases the likelihood for the infestation to spread and impact agricultural and municipal water systems that receive water from the river.

Weather station data acquired across multiple locations in the Teakettle Experimental Forest, California, 2011-2017

These weather station records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These weather station records are for studies at the Teakettle Experimental Forest (Lat 36.967, Long -119.017, elevation 2000-2800 m, www.fs.fed.us/psw/ef/teakettle/). Weather stations were located at six sites across the Teakettle Experimental Forest landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. Three full weather stations (north slope, south slope, and valley floor) monitored precipitation, wind, insolation, temperature, relative humidity, and soil moisture. Data were recorded on a 10-minute interval using HOBO (Onset, www.onsetcomp.com) devices.

Near-surface, soil, and air temperature data acquired across multiple locations in the foothills of the Tehachapi mountains at Tejon Ranch, California, 2011-2017

These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies in the foothills of the Tehachapi mountains at Tejon Ranch (Lat 34.983, Long -118.716, elevation 750-930 m, www.tejonranch.com). Temperature sensors were located at 23 sites across the Tehachapi foothills. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges and valleys. To characterize surface temperature variation within a site, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens. An additional 18 sensors were placed along three transects over the landscape running N-S. They were placed strategically to sample topographic inflection points (hill tops and valley bottoms) as well as north and south facing slopes. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor. using HOBO (Onset, www.onsetcomp.com) devices.

Weather station data acquired across multiple locations in the foothills of the Tehachapi mountains at Tejon Ranch, California, 2011-2017

These weather station records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These weather station records are for studies in the foothills of the Tehachapi mountains at Tejon Ranch (Lat 34.983, Long -118.716, elevation 750-930 m, www.tejonranch.com). Weather stations were located at six sites across the Tehachapi foothills. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. Three full weather stations (north slope, south slope, and valley floor) monitored precipitation, wind, insolation, temperature, relative humidity, and soil moisture. Three micro stations (west slope, east slope, and ridge) measured soil moisture at -20 cm. Data was recorded on a 10-minute interval using HOBO (Onset, www.onsetcomp.com) devices.

Near-surface, soil, and air temperature data acquired across multiple locations in the Tehachapi mountains at Tejon Ranch, California, 2011-2017

These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies in the Tehachapi mountains at Tejon Ranch (Lat 34.967, Long -118.583, elevation 1600-1700 m, www.tejonranch.com). Temperature sensors were located at 23 sites across the Tehachapi foothills. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges and valleys. To characterize surface temperature variation within a site, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens. An additional 18 sensors were placed along three transects over the landscape running N-S. They were placed strategically to sample topographic inflection points (hill tops and valley bottoms) as well as north and south facing slopes. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor. using HOBO (Onset, www.onsetcomp.com) devices.

Weather station data acquired across multiple locations in the Tehachapi mountains at Tejon Ranch, California, 2011-2017

These weather station records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These weather station records are for studies the Tehachapi mountains at Tejon Ranch (Lat 34.967, Long -118.583, elevation 1600-1700m, www.tejonranch.com). Weather stations were located at six sites across the Tehachapi foothills. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. Three full weather stations (north slope, south slope, and valley floor) monitored precipitation, wind, insolation, temperature, relative humidity, and soil moisture. Three micro stations (west slope, east slope, and ridge) measured soil moisture at -20 cm. Data was recorded on a 10-minute interval using HOBO (Onset, www.onsetcomp.com) devices.

A scrubbed subset of near-surface, soil, and air temperature data acquired across multiple locations on the San Joaquin Experimental Range, California, 2012-2017

These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies at the San Joaquin Experimental Range (Lat 37.083, Long -119.716, elevation 210-520 m, www.fs.fed.us/psw/ef/san_joaquin/). Temperature sensors were located at 23 sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. To characterize surface temperature variation within a site, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens. An additional 18 sensors were placed along three transects over the landscape running E-W. They were placed strategically to sample topographic inflection points (hill tops and valley bottoms) as well as north and south facing slopes. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor, using HOBO (Onset, www.onsetcomp.com) devices.

A scrubbed subset of near-surface, soil, and air temperature data acquired across multiple locations on Teakettle Experimental Forest, California, 2011-2017

These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies at the Teakettle Experimental Forest (Lat 36.967, Long -119.017, elevation 2000-2800 m, www.fs.fed.us/psw/ef/teakettle/). Temperature sensors were located at 44 sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges and valleys. To characterize surface temperature variation within select sites, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens (see garden schematic for details). An additional 33 sites were located across the site by way of a stratified sampling scheme which targeted low, medium, and high elevation areas, low, medium, and high radiation areas, and cold air pooling areas. In June 2012, in order to concentrate sensors in a smaller study area (ease of access and to make this more similar to other sites, 22 sites were "retired," and 7 new sites were installed, for a total of 18 during the remainder of the study. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor. using HOBO (Onset, www.onsetcomp.com) devices.

A scrubbed subset of near-surface, soil, and air temperature data acquired across multiple locations in the foothills of the Tehachapi mountains at Tejon Ranch, California, 2011-2017

A scrubbed subset of near-surface, soil, and air temperature data acquired across multiple locations in the Tehachapi mountains at Tejon Ranch, California, 2011-2017

These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies in the Tehachapi mountains at Tejon Ranch (Lat 34.967, Long -118.583, elevation 1600-1700 m, www.tejonranch.com). Temperature sensors were located at 23 sites across the Tehachapi foothills. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges and valleys. To characterize surface temperature variation within a site, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens. An additional 18 sensors were placed along three transects over the landscape running N-S. They were placed strategically to sample topographic inflection points (hill tops and valley bottoms) as well as north and south facing slopes. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor. using HOBO (Onset, www.onsetcomp.com) devices.

openCC (other)Jan 2025View details →

Long term egg thiamine monitoring in salmonid populations in California; 2020-2023

Monitoring of egg thiamine levels was initiated in California salmon and steelhead hatcheries in 2020 after thiamine deficiency complex (an insufficiency of vitamin B1) was first documented in this system resulting in widespread mortality of juvenile salmonids. Unfertilized eggs (~10g) from mature adult females were collected from populations of Chinook salmon ( Oncorhynchus tshawytscha ), steelhead ( Oncorhynchus mykiss ), and coho salmon ( Oncorhynchus kisutch ) across California to assess thiamine concentrations. Concurrent fork length, weight, as well as coded wire tag recovery information for Central Valley samples was recorded alongside egg thiamine concentration levels. Additionally, laboratory investigations have been undertaken to uncover the relationship between Chinook salmon egg thiamine concentration and the survival of offspring. From these findings we have understood the potential population-level impacts of thiamine-dependent Chinook salmon fry mortalities based on egg surveillance data. The annual monitoring of eggs from salmonid species in both Central Valley and coastal populations serves as a critical component in comprehending the prevalence, magnitude, and trends of this deficiency among California salmonids. This dataset is focused on supporting research and providing annual data to inform the public and resource managers responding to this emerging threat. Given the value of this information to managing salmonid resources and treatments, we expect this monitoring to continue into the future as funding allows.

openCC0Mar 2025View details →

California Motus Prioritization Tool Data

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 all the necessary files to recreate the data analysis, print out maps based on predictions

openCC (other)Mar 2025View details →

Microbial Sulfate Reduction Rates in Soils in the Napa River Watershed, California, USA, 2021-2023

Agricultural sulfur (S) inputs are a major source of anthropogenic S to the environment, often stimulating microbial sulfate reduction (MSR) in downstream environments, which can drive a cascade of unintended ecosystem consequences. This dataset includes samples collected throughout the Napa River Watershed, California, USA, where routine, high S applications to vineyards are common. Sampling was focused confirming the presence of microbial sulfate reduction (MSR) within upland soils, challenging the conventional view that this process is restricted to fully saturated environments. We collected soil samples for sulfate concentrations, sulfate reduction rates (SRRs), and organic C content (Loss On Ignition, LOI) under three different hydrological conditions: while soils were moist (November 2021), dry (January/February 2022), and saturated (January/February 2023). We collected samples from a variety of different land cover types, including vineyard, vineyard stream, grassland, forest, forest stream, and wetland.

openCC (other)Oct 2025View details →

Qualitative Larval Fish Sampling at the California Department of Water Resource’s State Water Project

The California Department of Water Resource’s State Water Project utilizes the John E. Skinner Delta Fish Protective Facility (Skinner Fish Facility) to salvage fishes that would otherwise become entrained during operations to divert water from the Sacramento-San Joaquin River Delta (Delta). Water is diverted from the Delta to meet California’s agricultural, municipal, industrial, and environmental needs. The Skinner Fish Facility, located in Contra Costa County and situated ahead of the Harvey O. Banks Pumping Plant, began salvaging fish in 1968 but historically, only recorded fork length measurements for fish greater than 20 millimeters. Beginning in 2009, the Skinner Fish Facility implemented qualitative larval sampling in response to the 2008 U.S. Fish and Wildlife Service Biological Opinion on the coordinated operations of the Central Valley Project (CVP) and State Water Project (SWP). This entailed collecting, retaining, and identifying larval fishes to better understand SWP impacts on Delta Smelt. Qualitative larval sampling took place annually from 2009 through 2025, during the Old and Middle River management period and based upon Delta Smelt spawning (typically mid-February to June). The California Department of Water Resources collected and processed samples from 2020 through 2025. Data from 2009 through 2019 were processed and retained by others and are not included in this dataset.

openCC (other)Jun 2022View details →

California Harmful Algal Bloom Monitoring and Alert Program Data (Darwin Core Archive format)

The Harmful Algal Bloom Monitoring and Alert Program (HABMAP) was formed in 2008 and provides updates on current algal blooms and facilitates information exchange among scientists, federal and state managers, and the general public in California. A major component of this program is regional HAB monitoring with support from the Southern California Coastal Ocean Observing System (SCCOOS) and the Central and Northern California Ocean Observing System (CeNCOOS). Water samples and net tows are collected once per week at piers to monitor for HAB species, the neurotoxin domoic acid, and water quality data including temperature, chlorophyll-a, and nutrients. The sampling stations represented in this dataset include Santa Cruz Wharf, Monterey Wharf, Cal Poly Pier, Stearns Wharf, Santa Monica Pier, Newport Beach Pier, and Scripps Pier. These data are consolidated and reformatted into Darwin Core Archive (DwC-A) format from the level 1 site-specific datasets hosted on the SCCOOS ERDDAP server: (https://erddap.sccoos.org/erddap/tabledap/index.html?page=1).

openCC0Aug 2025View details →

Chlorophyll and phaeopigments measured from discrete bottle samples from CCE LTER process cruises in the California Current System, determined by extraction and bench fluorometry, 2006 - 2024 (ongoing).

Discrete bottle samples taken from various depths in the CCE region are filtered (known volumes) onto GF/F filters onboard the CCE Process cruises (since 2006, ongoing). The filters are placed into culture tubes containing 90% acetone, and the fluorescence of the samples is read on a fluorometer after 24 to 48 hours. The samples are then acidified to degrade the chlorophyll to phaeopigments (non-photosynthetic pigments) and a second reading is taken. The readings prior to and after acidification are used to calculate concentrations of both chlorophyll a and phaeopigments (i.e. phaeophytin).