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Pelagic, epilimnetic production estimates in Sparkling, Trout (Wisconsin), Acton (Ohio), and Castle (California) Lakes (USA) calculated using 14C and free-water O2 metabolism methods, 2007 - 2017
Concurrent daily estimates of pelagic, eplilimnetic production (mmol C m3 d) generated from 14C incubations and diel changes in high frequency dissolved oxygen data (free-water). Original data derived from the North Temperate Lakes Long Term Ecological Research program (Sparkling [2007-2013], Trout [2007-2012] Lakes), Castle Lake Research Station (Castle Lake [2014-2017]), and Center for Aquatic and Watershed Sciences (Acton Lake [2010-2014]). 14C production estimates were generated as part of each research programs core data collection. Free-water production estimates generated using high frequency sensor data provided by research programs and Phillips (2020) time-varying, Bayesian metabolism model.
Juvenile Salmonid Emigration Monitoring in the Lower American River, California.
Overview Operation of rotary screw traps on the Lower American River is part of a collaborative effort by the U.S. Fish and Wildlife Service, Pacific States Marine Fisheries Commission, and the California Department of Fish and Wildlife. 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 steelhead Oncorhynchus mykiss as well as winter, spring, and late fall runs of Chinook Salmon. 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. The data package contains seven datasets including: raw catch, trap operation, environmental, and trap efficiency data. Raw Catch – Chinook Dataset This dataset covers ALL Chinook Salmon captured by the rotary screw traps. This spreadsheet includes biological data on: 1) unmarked fall-, spring-, and winter-run Chinook Salmon 2) marked (adipose clipped OR "fin clip") hatchery origin Chinook Salmon 3) recaptured marked fall-run (BBY OR "Pigment / Dye", Photonic Dye, and VIE OR "Elastomer") Chinook Salmon utilized in trap efficiency trials. Raw Catch – Steelhead Dataset This dataset covers ALL steelhead captured by the rotary screw traps. This spreadsheet includes biological data on: 1) unmarked (natural origin) steelhead 2) marked (adipose clipped OR "fin clip") hatchery origin steelhead 3) recaptured marked steelhead utilized in trap efficiency trials. Raw Catch – ByCatch Dataset This dataset provides biological data on ALL catch (EXCLUDING Chinook Salmon or steelhead) captured by the rotary screw traps. All catch in this table is of natural origin. Trap Operations Dataset This dataset provides trap operation data for each trap visit. Specifically, it includes data on the visit
Lower American River steelhead and Chinook stranding surveys, California, 2016 - 2025
Steelhead stranding surveys have been conducted on the Lower American River (LAR) for the years 2016-2025. Reclamation’s mission is to manage, develop and protect water and related resources in an environmentally and economically sound manner in the interest of the American people. In the National Marine Fisheries Service (NMFS) most recent biological opinion (2009), the presence of dams was identified as the most influential stressor to steelhead on the American River because it blocks passage to historic spawning and rearing habitat. Thus, Reclamation is required to monitor the effects of flow regulation by dams on the steelhead life stages present in the river system. Congruently, Reclamation has committed to significant restoration actions including salmonid spawning and rearing habitat rehabilitation on the Lower American River, which also require accurate and robust monitoring. These surveys support the mission and monitoring requirements of Reclamation by collecting the stranding data required to effectively conduct analyses of the effects of regulating Folsom and Nimbus dams on this federally listed species’ critical life stage development and support operational decision making.
Juvenile Salmonid Emigration Monitoring in the Stanislaus River at Caswell Memorial State Park, California, 2017-2025
Overview Operation of rotary screw traps on the lower Stanislaus River at Caswell Memorial State Park is part of the U.S Fish and Wildlife Service’s Anadromous Fish Restoration Program and Comprehensive Assessment and Monitoring Program under the National Marine Fisheries Service Reasonable and Prudent Alternatives actions and Central Valley Project Improvement Act. 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 steelhead 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. The data package contains seven datasets including: raw catch, trap operation, environmental, and trap efficiency data. Raw Catch – Chinook Dataset This dataset covers ALL Chinook Salmon captured by the rotary screw traps. This spreadsheet includes biological data on: 1) unmarked fall- and spring-run Chinook Salmon 2) recaptured marked fall-run (BBY OR "Pigment / Dye", Photonic Dye, Fin Clip, and VIE OR "Elastomer") Chinook Salmon utilized in trap efficiency trials. Raw Catch – Steelhead Dataset This dataset covers ALL steelhead captured by the rotary screw traps. All steelhead captured are unmarked and presumed to be natural origin steelhead. Raw Catch – ByCatch Dataset This dataset provides biological data on ALL catch (EXCLUDING Chinook Salmon or steelhead) captured by the rotary screw traps. All catch in this table is of natural origin. Trap Operations Dataset This dataset provides trap operation data for each trap visit. Specifically, it includes data on the visit type, trap functioning status, start and end sampling dates and times, total revolutions and instantaneous revolution speeds, livewell intake st
Data from: Satellite-based Lagrangian model reveals how upwelling and oceanic circulation shape krill hotspots in the California Current System [updated]
<p><strong>Abstract</strong></p> <p>In the California Current System, wind-driven nutrient supply and primary production, computed from satellite data, provide a synoptic view of how phytoplankton production is coupled to upwelling. In contrast, linking upwelling to zooplankton populations is difficult due to relatively scarce observations and the inherent patchiness of zooplankton. While phytoplankton respond quickly to environmental forcing, zooplankton grow slower and tend to aggregate into mesoscale “hotspot” regions spatially decoupled from upwelling centers. To better understand mechanisms controlling the formation of zooplankton hotspots, we use a satellite-based Lagrangian method where variables from a plankton model, forced by wind-driven nutrient supply, are advected by near-surface currents following upwelling events. Modeled zooplankton distribution reproduces published accounts of euphausiid (krill) hotspots, including the location of major hotspots and their interannual variability. This satellite-based modeling tool is used to analyze the variability and drivers of krill hotspots in the California Current System, and to investigate how water masses of different origin and history converge to form predictable biological hotspots. The Lagrangian framework suggests that two conditions are necessary for a hotspot to form: a convergence of coastal water masses, and above average nutrient supply where these water masses originated from. The results highlight the role of upwelling, oceanic circulation, and plankton temporal dynamics in shaping krill mesoscale distribution, seasonal northward propagation, and interannual variability.</p> <p><strong>Data set description</strong></p> <p>This data set includes 2 files:</p> <ul> <li>a satellite-based 1993-2023 monthly retrospective of krill concentrations (Zbig) modeled using the growth-advection method in the California Current upwelling system. Inputs include the nitrate supply product described below and GlobCurrent 15 m oceanic currents. This dataset is updated monthly (using NRT data) at https://www.mbari.org/science/upper-ocean-systems/biological-oceanography/krill-hotspots-in-the-california-current/.</li> <li>a satellite-based 1993-2023 monthly retrospective of wind-driven nitrate supply estimated in a 150 km coastal band at 0.125° latitudinal resolution. Nitrate supply was calculated based primarily on CCMP v3.1 winds, AVISO geostrophic currents, and a climatology of in situ nitrate at 60m. This dataset is updated monthly (using NRT data) at https://www.mbari.org/science/upper-ocean-systems/biological-oceanography/nitrate-supply-estimates-in-upwelling-systems/.</li> </ul> <p>See details regarding data sources and calculations in <a href="https://doi.org/10.3389/fmars.2022.835813">Messié et al. (2022)</a>.</p> <p>[IMPORTANT NOTE:] There is an error in the Ekman pumping fields (trans_pump, Nsupply_pump, Nsupply_total) that will be corrected soon (those fields are not used in publications where only coastal transport was considered). Please contact me if you need Ekman pumping fields before this is fixed.</p>
Lower American River steelhead spawning surveys (Chinook and lamprey data included), California, 2002 to 2025
Steelhead spawning surveys have been conducted on the Lower American River (LAR) for the years 2002-2005, 2007, and 2009-2025. These surveys in conjunction with annual escapement estimates to Nimbus Fish Hatchery, are used to provide a yearly index of in-river and over all spawning abundance. Reclamation’s mission is to manage, develop and protect water and related resources in an environmentally and economically sound manner in the interest of the American people. In the National Marine Fisheries Service (NMFS) most recent biological opinion (2009), the presence of dams was identified as the most influential stressor to steelhead on the American River because it blocks passage to historic spawning and rearing habitat. Thus, Reclamation is required to monitor the effects of flow regulation by dams on the steelhead life stages present in the river system. Congruently, Reclamation has committed to significant restoration actions including salmonid spawning and rearing habitat rehabilitation on the Lower American River, which also require accurate and robust monitoring. These surveys support the mission and monitoring requirements of Reclamation by collecting the spawning data required to effectively conduct analyses of the effects of regulating Folsom and Nimbus dams on this federally listed species’ critical life stage development and support operational decision making.
Anatoxin concentrations, algal assemblages, and water quality data for the South Fork Eel, Salmon, and Russian Rivers in northern California, 2022-2023
We collected this data to better understand the timing of peak benthic cyanobacterial mat occurrence (specifically taxa associated with anatoxin production, Microcoleus and Anabaena) and mat anatoxin concentrations in rivers. We sampled in northern California on the South Fork Eel, Salmon, and Russian Rivers biweekly in 2022, and the Salmon River biweekly and South Fork Eel weekly in 2023. During each sampling event, we conducted benthic cover surveys, measured in-situ water quality parameters (temperature, pH, dissolved oxygen, conductivity), and collected surface water samples and targeted cyanobacteria samples. In 2022 on all rivers and in 2023 at the Salmon River, we also collected distributed non-targeted periphyton samples to characterize full-reach community compositions. All sampling was completed in 150-m reaches upstream of sensors recording continuous dissolved oxygen, conductivity, and temperature data. We analyzed surface water samples for nitrate, ammonium, soluble reactive phosphate, total dissolved carbon, and dissolved organic carbon. We also analyzed surface water samples from 2022 for major anions (Cl, SO4, Br) and cations (Na, K, Mg, Ca). Targeted-cyanobacteria and non-target periphyton samples were analyzed for anatoxins (and two other classes of toxins, microcystins and cylindrospermopsins), relative abundance of algal taxa (via microscopy), ash-free dry mass, and chlorophyll-a. To estimate mean river depth within the dissolved oxygen footprint upstream of sensors, we kayaked portions of the river and collected river depth measurements. We also measured discharge at each river excluding the Salmon River (due to high discharge) and completed pebble counts at the South Fork Eel River to obtain sediment grain size distributions. Lastly, we estimated daily reach-scale river metabolism (gross primary productivity and ecosystem respiration) using data from dissolved oxygen sensors with the "streamMetabolizer" package in R at all sensor placements.
Relative predation rates on juvenile Chinook Salmon in the lower Stanislaus River, California, 2012-2024 by habitat suitability informed by juvenile Chinook Salmon and black bass observations in the lower Stanislaus and Merced rivers, California, 2012-2017
Overview The purpose of this work was to estimate relative predation on juvenile Chinook Salmon rearing in tributaries of the San Joaquin River, California in relation to meso- and microhabitat factors. Predation rates were estimated using predation bioassays. Ranges of depth and velocity targeted by the bioassays were informed by habitat suitability indices developed prior to field efforts. Juvenile Chinook and Bass Habitat Suitability Indices The purpose of this dataset is to develop habitat suitability indices for juvenile Chinook Salmon (<120mm) on the lower Stanislaus River and nonnative black bass ( Micropterus spp.). on the lower Merced River, both tributaries of the San Joaquin. This data was used to identify target ranges of depth and velocity during predation fieldwork. Occupancy data was collected via snorkel surveys on the lower Stanislaus River in 2018 and 2019 and on the Merced River in 2012 and 2014-2017. Predation Tethering Bioassay Study The purpose of this field study was to estimate relative rates of predation of juvenile Chinook Salmon. Predation rates were estimated using assays of tethered hatchery Chinook Salmon deployed across a range of mesohabitats on the lower Stanislaus River. Habitat suitability was expected to vary across mesohabitats and across depths and velocities sampled within habitats. Cameras were deployed with tethers to identify predators for a subset of predation events happening within the first 1-2 hours of deployment. Assays were deployed monthly March-May in 2022 and 2024. A supplemental set of assays were deployed in May 2023 under wet water year conditions that varied strongly from conditions sampled in 2022 and 2024.
2021-2024 Juvenile Chinook Salmon Rearing and Growth on the Lower American River, California
The primary goal of the Central Valley Project Improvement Act is to at least double natural production of Chinook Salmon ( Oncorhynchus tshawytscha ) in California Central Valley (CCV) streams on a sustainable basis. Beginning in 2008, semi-annual gravel augmentation and off channel habitat enhancement projects were implemented on the Lower American River (LAR) by Reclamation and USFWS, in partnership with the Sacramento Water Forum, as part of the LAR habitat enhancement program. The overall vision for the habitat enhancement program is to restore ecosystem processes by rehabilitating and enhancing critical channel, floodplain, and riparian habitats for juvenile and adult anadromous salmonids, thus promoting the recovery of healthy and diverse Chinook Salmon and steelhead ( O. mykiss ) populations. Off channel rearing habitat has been identified as a limiting factor in meeting CCV salmon population goals. While numerous studies have documented positive relationships between off channel habitat and juvenile rearing on the LAR, it is not known how long juveniles remain in off channel habitat compared with the main channel, whether rearing in off channel habitat enhances growth compared with the main channel, whether the relative value of off channel habitat for juvenile production depends on how long it has been inundated, or whether juvenile diet in off channel habitat differs from that in the main channel. To better understand these relationships, we conducted a mark-recapture study under a range of hydrological conditions between 2021-2024 using passive integrated transponder (PIT) tagged wild juvenile Chinook Salmon coupled with seining surveys at five off channel restoration sites on the LAR designed for rearing, as well as nearby main channel control sites that were also suitable rearing habitat. First, we investigated whether side channel habitats in restored reaches support higher Chinook Salmon densities than main channel control habitats. Density was estim
Estimated Inundation Periods in the Yolo Bypass, California, 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. 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. YBFMP’s data is often accompanied by information on whether the Yolo Bypass is inundated, as water quality, and species composition and abundance can be greatly altered during inundation. This dataset was created to consistently estimate inundation over time. Estimating
Fish Food on Floodplain Farm Fields, California Central Valley, Seasons 2019 and 2021
2019 Water Year (October 1, 2018 through September 30, 2019) In the winter and spring of 2018-2019, 5,000 acres of agricultural land in Yolo County, California was intentionally flooded. These “dry-side” rice fields, although on the former floodplain of the Sacramento River, are separated from the fish-bearing Sacramento River (the “wet-side”) by high flood levees. Today, levees cut off 95% of the Central Valley’s floodplains from river channels so that Central Valley aquatic ecosystems no longer recruit floodplain the food web resources needed to support robust aquatic food webs, create fish biomass and sustain abundant fish populations. In this experiment we asked whether floodplain food web resources “grown” in intentionally inundated “dry-side” agricultural fields could be exported back to the river via flood drainage infrastructure. If so, we were interested to know whether those resources could improve juvenile salmon foraging success and increase growth rates. In order to test these questions, we caged fish in the floodplain drainage canal, at the location where the floodplain drainage water entered the river and at locations both up- and downstream. We hypothesized that zooplankton abundance and fish growth rates would be elevated at the managed floodplain outfall location, relative to the upstream location. We measured water quality parameters, zooplankton species assemblage and abundance, and juvenile Chinook salmon growth rates with PIT tagged, hatchery-origin fish confined to enclosures at the study locations. The 5,000 acres of managed floodplain was drained over the coarse of 5 weeks in February and March, 2019 at a maximum rate of 1,000 cfs. The Sacramento River flow during the experiment ranged from 20,000-30,000 cfs. Fish growth rates at the floodplain outfall location were up to five times greater than growth rates upstream of the outfall and enclosure fish experienced growth rate benefits at least up to a mile downstream from the managed floodplai
Leaf Traits of Darlingtonia Californica in Oregon and California 2001
Scaling relationships among photosynthetic rate, foliar nutrient concentration, and leaf mass per unit area (LMA) have been observed for a broad range of plants. Leaf traits of the carnivorous pitcher plant Darlingtonia californica, endemic to southern Oregon and northern California, USA, differ substantially from the predictions of these general scaling relationships; net photosynthetic rates of Darlingtonia are much lower than predicted by general scaling relationships given observed foliar nitrogen (N) and phosphorus (P) concentrations and LMA. At five sites in the center of its range, leaf traits of Darlingtonia were strongly correlated with elevation and differed with soil calcium availability and bedrock type. The mean foliar N : P of 25.2 6 15.4 of Darlingtonia suggested that these plants were P-limited, although N concentration in the substrate also was extremely low and prey capture was uncommon. Foliar N : P stoichiometry and the observed deviation of Darlingtonia leaf traits from predictions of general scaling relationships permit an initial assessment of the "cost of carnivory" in this species. Carnivory in plants is thought to have evolved in response to N limitation, but for Darlingtonia, carnivory is an evolutionary last resort when both N and P are severely limiting and photosynthesis is greatly reduced.
Fish Facilities Salvage Data, San Francisco, California, 1993-2024
The Bureau of Reclamation’s (Reclamation) Central Valley Project (CVP) and the California Department of Water Resource’s (DWR) State Water Project (SWP) deliver millions of acre-feet of water annually for agricultural, municipal, industrial, and environmental needs in California from the Sacramento-San Joaquin River Delta (Delta) through the C.W. “Bill” Jones Pumping Plant (JPP) and Banks Pumping Plant. Since 1957, a Reclamation operated fish salvage facility, the Tracy Fish Collection Facility (TFCF), is located upstream of the JPP and functions to salvage fish entrained in exported water (Bates and Vinsonhaler 1957). Additionally, the John E. Skinner Delta Fish Protective Facility (SDFPF) was added by the California Department of Water Resources in 1968 to salvage fishes diverted by the SWP. The salvage process involves fish collection, counting, handling and transportation back to the Delta. To prevent fish loss, CVP and SWP fish facilities were constructed at Old river, where fish are diverted to the fish facilities for counting and reporting. After counting, the fish are collected in storage tanks and taken to several release locations in the Delta via fish-haul tank trucks. Millions of fishes from 69 species are salvaged through this process by the two fish facilities. Data collected includes species collected, fish lengths, water flow, export amounts, and water quality. Fishes listed (Endangered Species Act (ESA) or California Endangered Species Act (CESA)) were Chinook Salmon, Delta Smelt, steelhead trout, Longfin Smelt, and Green Sturgeon. The California Department of Fish and Wildlife monitors fish salvage and manages the data collected from the fish facilities in addition to data collected and managed by DWR and Reclamation.
Near-surface, soil, and air temperature data acquired across multiple locations on the San Joaquin Experimental Range, 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 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.
Weather station data acquired across multiple locations on the San Joaquin Experimental Range, 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 San Joaquin Experimental Range (Lat 37.083, Long -119.716, elevation 210-520 m, www.fs.fed.us/psw/ef/san_joaquin/). Weather stations were located at six 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. 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 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.
California Department of Fish and Wildlife Adult Sturgeon Study, Sacramento-San Joaquin Watershed, 1954-2022
The Sacramento-San Joaquin Watershed, located in Central and Northern California, drains approximately 43,000 square miles and terminates at the Golden Gate Bridge. This watershed hosts numerous species of ecological, cultural, and recreational importance, including White (Acipenser transmontanus) and Green Sturgeon (Acipenser medirostris). Sturgeon were severely overfished in the late 1800s and early 1900s, prompting a closure of the recreational and commercial sturgeon fishery in 1917 by the California Department of Fish and Game (CDFG; Now California Department of Fish and Wildlife, CDFW). The fishery remained closed until 1954, when a recreational fishery was once again allowed by the CDFG. A single year of surveying was conducted by the CDFG in 1954 to monitor the new fishery and a semi-regular survey was established in 1967. Since then, CDFW has systematically surveyed subadult and adult White and Green Sturgeon as part of the Adult Sturgeon Study, with annual surveys conducted between 2005 and 2022. Capturing adult sturgeon using 3.7m deep drifted trammel nets in areas including Suisun Bay, Grizzly Bay, and San Pablo Bay, these efforts have been supplemented by angler-contributed data, collected through mail returns and river/bay creel surveys. Tagging practices involve individually coded ½” Petersen-disk tags, with reward values introduced in 1974 to encourage angler cooperation and enhance tag return rate accuracy. The adoption of PIT (Passive Integrated Transponder) tags began in 2007 and has been consistently employed since 2019. These data provide insights into tag return rates, recaptures, and mortalities, supporting the estimation of abundance and harvest rates. This comprehensive dataset enriches our understanding of sturgeon population dynamics and is crucial for monitoring California sturgeon.
Juvenile salmonid rotary screw trap data from Battle and Clear Creeks, Shasta and Tehama Counties, California.
Clear Creek The U.S. Fish and Wildlife Service continued its juvenile salmonid monitoring project in Clear Creek, Shasta County, California, that began in December 1998 using a rotary screw trap (RST) located at river mile (RM) 1.7. This monitoring project has three primary objectives: (1) calculate annual juvenile passage indices for Chinook Salmon Oncorhynchus tshawytscha and Rainbow Trout/steelhead O. mykiss (we use the term O. mykiss to refer to both the stream resident (Rainbow Trout) and anadromous (steelhead) life histories because of the difficulties in differentiating the anadromous and resident forms in the field) for inter-year comparisons and analyses of the effectiveness of stream restoration activities; (2) obtain juvenile salmonid life history information including size, timing, and potential factors limiting survival; and (3) collect biological samples from juvenile salmonids. Chinook Salmon run classifications show that all Chinook Salmon runs known to the Sacramento River were captured; however, due to overlapping spawning times of spring-run and fall-run Chinook Salmon it was problematic to index the juvenile passage using only the RST at RM 1.7. Since 2003 a separation weir has been used to isolate adult spring-run Chinook Salmon from adult fall-run Chinook Salmon; therefore, a second RST was added above the weir at RM 8.4. Battle Creek The U.S. Fish and Wildlife Service continued its juvenile salmonid monitoring project in Battle Creek, Shasta and Tehama Counties, California, that began in December 1998 using a RST located at river mile (RM) 6.2. The upper Battle Creek RST objectives are to (1) calculate annual juvenile passage indices for spring-run, late-fall run, and winter-run Chinook Salmon; Rainbow Trout/steelhead O. mykiss (we use the term O. mykiss to refer to both the stream resident (Rainbow Trout) and anadromous (steelhead) life histories because of the difficulties in differentiating the anadromous and resident forms in the field); (
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.
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
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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.