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An unmanned aerial system (UAS) was used to acquire red/green/blue (RGB) and hyperspectral image data from the American River in California November 5-7, 2018, to support research on remote sensing of rivers, specifically mapping chinook salmon spawning locations (redds) as part of an overall salmon habitat assessment program. The RGB images were acquired uisng a DJI MAtrice 210 equipped with a Zenmuse 4S optical camera. Imagery was collected along several parallel flight lines to ensure full coverage of the study reach. Raw Zenmuse images were georeferenced using real-time kinematic (RTK) global positioning system (GPS) and inertial motion unit (IMU) data recorded onboard the UAS and individual flight strips were...
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This child data release includes field spectra obtained as part of a study focused on mapping chinook salmon spawning locations along the American River near Sacramento, California, via remote sensing; the data were collected November 5-7, 2018. The purpose of this study was to develop and test a spectrally based technique for identifying salmon spawning locations, known as redds, from various types of remotely sensed data. Traditionally, redds have been mapped by eye while walking the bank or from a boat, or by an observer in an aircraft or an interpreter visually examining aerial images. The goal of this proof-of-concept investigation was to assess the potential for more efficient, objective, and automated...
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Physical and chemical changes affect the biota within urban streams at varying scales ranging from individual organisms to populations and communities creating complex interactions that present challenges for characterizing and monitoring the impact on species utilizing these freshwater habitats. Salmonids, specifically cutthroat trout (Oncorhynchus clarkii) and coho salmon (Oncorhynchus kisutch), extensively utilize small stream habitats influenced by a changing urban landscape. This study used a comprehensive fish health assessment concurrent with the U.S. Geological Survey’s Pacific Northwest Stream Quality Assessment in 2015 to quantifiy impacts from disease in juvenile coho and cutthroat salmon, impacts to...
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The U.S. Geological Survey (USGS) developed a regression model for estimating mean August baseflow per square mile of drainage area in cooperation with National Oceanic and Atmospheric Administration (NOAA) to help resource managers assess relative amounts of baseflow in streams with Maine Atlantic Salmon habitat (Lombard and others, 2021). The model was applied to each reach of a stream network derived from select National Hydrography Dataset Plus High-Resolution (NHDPlusHR) data in the State of Maine south of 46º 21′55″ N latitude. The spatial coverage developed from the stream network contains model-estimated mean August baseflow per square mile of drainage area as an attribute of each NHDPlusHR reach. Please...
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To support an investigation of the effectiveness of a large-scale river restoration project, several types of field data were collected from two gravel-bed reaches of the regulated lower Merced River in California's Central Valley, primarily in the fall of 2016. These data sets were intended to characterize salmon spawning habitat and identify factors influencing spawning site selection. This parent data release includes links to child pages for the following data sets: 1) Bulk samples of streambed sediment used to characterize the subsurface grain size distribution. 2) Pebble counts used to characterize the sediment grain size distribution of the bed surface. 3) Force gage measurements used to parameterize a...
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Surveys of channel and floodplain topography were used to characterize the morphology of two reaches of the lower Merced River in California's Central Valley and to parameterize a hydraulic model. These data were collected to support research intended to evaluate the extent to which large-scale restoration projects provided improved salmon spawning habitat. A related goal of this study was to improve our understanding of the geomorphic factors influencing spawning site selection by salmon. At the Merced River Ranch field site, river channel and floodplain topography was measured using a combination of real-time kinematic (RTK) GPS for wadable parts of the channel, an echo sounder for deep pools, and photogrammetry...
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The data support a study that surveyed the spatial and temporal distribution of salmon eDNA in Seattle urban creeks, Washington, 2018 - 2020. The metadata represent qPCR quantification cycle (Cq) values for Chinook salmon, coho salmon, and coastal cutthroat trout assays performed on water samples collected on specific days at specific sites on Thornton Creek, Taylor Creek, and Mapes Creek, which are tributaries of Lake Washington within Seattle city limits. The metadata also includes latitude and longitude for each site and Y-intercept and slope for each assay run.
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We collected environmental DNA (eDNA) data from the Elwha River, home to the world’s largest dam removal project, to track the spatial and temporal patterns of species responses following dam removal. In total, we collected data for 11 different fish taxa, sampled at 25 sites ranging across 56 river kilometers in a wilderness river for 4 years following dam removal. We show that eDNA can effectively be used to determine whether fish have recolonized past former dams, and in some cases determine the spatial extent of that recolonization.
The shapefile contains the data necessary to recreate the analyses used in Jalbert et al., in review, Vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in southcentral Alaska. Specifically, users will be able to view 1) intrinsic potential model calculations for 5 Pacific salmonids (Chinook, chum, pink, sockeye, and coho salmon) and northern pike and 2) all parent nodes of the vulnerability model (human colonization, natural colonization, and habitat overlap) as well as their inputs. Finally, users are able to map vulnerability to invasion for each Pacific salmon species.
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The data contain yearly modeled estimates of Pacific salmon escapement (in annual metric tons of wet mass) from 1976 to 2015 across four regions of western North America. A second data file contains modeled estimates of contaminant or nutrient concentrations in Pacific Salmon. The modeled estimates were derived from Bayesian generalized linear models (contaminant or nutrient concentrations) or from Bayesian generalized additive models (Salmon Escapement).
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Bulk samples of streambed sediment were collected from two reaches of the lower Merced River in California's Central Valley to support research intended to evaluate the extent to which large-scale restoration projects provided improved salmon spawning habitat. A related goal of this study was to improve our understanding of the geomorphic factors influencing spawning site selection by salmon. The bulk samples were acquired during the summer of 2016 at the Merced River Ranch and Robinson Reach field sites using a McNeil sampler [McNeil and Ahnell, 1964]. Before collecting each sample, the surface layer was removed to avoid including surface grains as part of the sample. Surface material was scraped off to a depth...
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Pebble counts were used to characterize the sediment grain size distribution of the bed surface for two reaches of the lower Merced River in California's Central Valley to support research intended to evaluate the extent to which large-scale restoration projects provided improved salmon spawning habitat. A related goal of this study was to improve our understanding of the geomorphic factors influencing spawning site selection by salmon. The pebble counts were performed at the Merced River Ranch and Robinson Reach field sites using the method of Wolman [1954]. Grain diameters (n>100) were measured using a gravelometer by recording the largest opening on the gravelometer that an individual particle did NOT pass...
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Understanding how routing modifications influence survival of juvenile salmon is complex because reach-specific survival and routing at key river junctions in the North Delta each have a different relationship with river flow. Therefore, to facilitate understanding of how routing modifications at key river junctions influence through-Delta survival, we developed this spreadsheet model to allow managers to explore the potential effects of modifying routing. The purpose is to provide a screening tool that allows managers to quickly run many different scenarios to understand how both routing and route-specific survival interact to affect overall survival through the Delta. This tool may be useful in narrowing the range...
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Field measurements of saturated hydraulic conductivity were used to characterize the streambed permeability for two reaches of the lower Merced River in California's Central Valley to support research intended to evaluate the extent to which large-scale restoration projects provided improved salmon spawning habitat. A related goal of this study was to improve our understanding of the geomorphic factors influencing spawning site selection by salmon. Saturated hydraulic conductivity, denoted by K, was measured with a backpack permeameter and modified Mark VI groundwater standpipe using the constant head method of Terhune [1958]. For each reach, permeameter measurements were collected at ten sites spanning a single...
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We used snorkel surveys in the Elwha River, conducted in consecutive years before (2007, 2008) and after (2018, 2019) dam removal to assess changes in fish distribution and density. In total, we counted 54,616 Chinook Salmon, Bull Trout, Steelhead, and trout (Rainbow Trout and Coastal Cutthroat Trout combined) in 22 common reaches spanning 65 river kilometers. The occupancy of juvenile Chinook Salmon, Coho Salmon, and trout was also assessed following dam removal.
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Field measurements of water depth were acquired from a reach of the upper American River in California, November 5-7, 2018, to support research on mapping chinook salmon spawning locations (redds) via remote sensing. The depth measurements included in this data release were obtained by wading the shallow channel margins with RTK GPS receivers and measuring water surface elevations along the water's edge and bed elevations within the channel; depths were calculated by subtracting bed elevations from the nearest water surface elevation. For the deeper areas representing most of the channel, depths were recorded along a series of cross-sections by a SonTek RiverSurveyor S5 acoustic Doppler current profiler (ADCP) deployed...
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This data release includes images and field measurements used to map chinook salmon spawning locations along the American River near Sacramento, California, via remote sensing; the data were collected November 5-7, 2018. The purpose of this study was to develop and test a spectrally based technique for identifying salmon spawning locations, known as redds, from various types of remotely sensed data. Traditionally, redds have been mapped by eye while walking the bank or from a boat, or by an observer in an aircraft or an interpreter visually examining aerial images. The goal of this proof-of-concept investigation was to assess the potential for more efficient, objective, and automated redd mapping from conventional...
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This data release includes images and field measurements used to map chinook salmon spawning locations along the American River near Sacramento, California, via remote sensing; the data were collected November 5-7, 2018. The purpose of this study was to develop and test a spectrally based technique for identifying salmon spawning locations, known as redds, from various types of remotely sensed data. Traditionally, redds have been mapped by eye while walking the bank or from a boat, or by an observer in an aircraft or an interpreter visually examining aerial images. The goal of this proof-of-concept investigation was to assess the potential for more efficient, objective, and automated redd mapping from conventional...
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Force gage measurements were used to parameterize a force balance model for the initiation of sediment motion and thus characterize bed mobility for two reaches of the lower Merced River in California's Central Valley. These data were acquired to support research intended to evaluate the extent to which large-scale restoration projects provided improved salmon spawning habitat. A related goal of this study was to improve our understanding of the geomorphic factors influencing spawning site selection by salmon. The force gage measurements were made at the Merced River Ranch and Robinson Reach field sites and involved using a spring-resisting force gage to push a given submerged particle in a bed-parallel downstream...
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Salmon spawning locations (redds) were mapped to characterize habitat use along two reaches of the lower Merced River in California's Central Valley and thus support research intended to evaluate the extent to which large-scale restoration projects provided improved salmon spawning habitat. A related goal of this study was to improve our understanding of the geomorphic factors influencing spawning site selection by salmon. Salmon redds were mapped during the fall of 2016 at the Merced River Ranch and Robinson Reach field sites using real-time kinematic (RTK) GPS. The location of the center of each redd was surveyed in the UTM Zone 10/NAD83 coordinate system, with easting and northing coordinates recorded in units...
map background search result map search result map Evaluating Coho Salmon in Streams Across an Urbanization Gradient—Part 1, Growth Potential Based on Environmental Factors and Bioenergetics Field measurements for characterizing salmon spawning habitat in two restored reaches of the lower Merced River, California Surveys of channel bed topography from two restored reaches of the lower Merced River, California Bulk samples of streambed sediment from two restored reaches of the lower Merced River, California Pebble count-based bed surface sediment grain size distributions from two restored reaches of the lower Merced River, California Force gage measurements to characterize bed mobility in two restored reaches of the lower Merced River, California Measurements of streambed permeability from two restored reaches of the lower Merced River, California Salmon spawning locations (redds) in two restored reaches of the lower Merced River, California Image data and field measurements used to map salmon spawning locations via remote sensing, American River, California, November 5-7, 2018 Field spectra from salmon spawning locations on the American River, California, November 5-7, 2018 Hyperspectral and RGB image data used to map salmon spawning locations on the American River, California, November 5-7, 2018 Salmon spawning locations (redds) mapped in the field along the American River, California, November 5-7, 2018 Field measurements of water depth from the American River, California, November 5-7, 2018 Environmental DNA (eDNA) is an Effective Tool to Track Recolonizing Migratory Fish Following Large-Scale Dam Removal, field data Data describing vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in southcentral Alaska, 2017-2019 Riverscape snorkeling surveys of salmonid distribution and abundance before (2007, 2008) and after (2018, 2019) dam removal on the Elwha River, Washington Spatial Coverage for Estimated Baseflow for Streams Containing Endangered Atlantic Salmon in Maine, USA (version 1.1, June 2022) Spatial and temporal surveys of salmon eDNA in Seattle urban creeks, Washington, 2018 - 2020 The North Delta Routing and Survival Management Tool Modeled Pacific salmon escapement biomass and nutrient and contaminant concentrations across western North America, 1976-2015 Field spectra from salmon spawning locations on the American River, California, November 5-7, 2018 Hyperspectral and RGB image data used to map salmon spawning locations on the American River, California, November 5-7, 2018 Salmon spawning locations (redds) mapped in the field along the American River, California, November 5-7, 2018 Field measurements of water depth from the American River, California, November 5-7, 2018 Image data and field measurements used to map salmon spawning locations via remote sensing, American River, California, November 5-7, 2018 Surveys of channel bed topography from two restored reaches of the lower Merced River, California Pebble count-based bed surface sediment grain size distributions from two restored reaches of the lower Merced River, California Bulk samples of streambed sediment from two restored reaches of the lower Merced River, California Field measurements for characterizing salmon spawning habitat in two restored reaches of the lower Merced River, California Measurements of streambed permeability from two restored reaches of the lower Merced River, California Salmon spawning locations (redds) in two restored reaches of the lower Merced River, California Force gage measurements to characterize bed mobility in two restored reaches of the lower Merced River, California The North Delta Routing and Survival Management Tool Evaluating Coho Salmon in Streams Across an Urbanization Gradient—Part 1, Growth Potential Based on Environmental Factors and Bioenergetics Spatial Coverage for Estimated Baseflow for Streams Containing Endangered Atlantic Salmon in Maine, USA (version 1.1, June 2022) Data describing vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in southcentral Alaska, 2017-2019 Modeled Pacific salmon escapement biomass and nutrient and contaminant concentrations across western North America, 1976-2015