Filters: partyWithName: Ecosystems (X) > partyWithName: Western Fisheries Research Center (X)

Filters Date Range Past year (22) Past month (1) Past week (0) Past day (0) Custom range... To   Search Extensions Shapefile (2) ArcGIS Service Definition (1) Citation (1) Types Map Service (9) OGC WFS Layer (8) OGC WMS Layer (8) OGC WMS Service (6) Downloadable (3) More... Contacts U.S. Geological Survey - ScienceBase U.S. Geological Survey Carl O Ostberg Maureen Purcell Jeffrey Duda More... Categories Data (54) Data Release - Revised (4) Publication (1) Tag Types Theme (56) Place (53) USGS Scientific Topic Keyword (47) Harvest Set (58) Catalog Filter Data Theme (1) Keyword (1) Catalog Filter Data Type (1) More... Tag Schemes None (21) USGS Thesaurus (33) ISO 19115 Topic Category (39) Common geographic areas (24) Getty Thesaurus of Geographic Names (4) https://www.sciencebase.gov/vocab/category/bis/NFHP%20Data%20Catalog%20 (1) Geographic Names Information System (GNIS) (2) More... View Results as: JSON ATOM CSV

Data relating to the development of a quantitative PCR assay for detecting Northwest salamander (Ambystoma gracile) in environmental DNA samples The data support a study that describes the development and validation of a primer and probe based quantitative PCR (qPCR) assay for use with environmental DNA to detect Northwest salamander (Ambystoma gracile), a species endemic to the temperate Pacific coastal region of North America. The metadata includes qPCR quantification cycle (Cq) values from testing the A. gracile assay on DNA extracted from tissue samples derived from several A. gracile and closely related species and Cq values from testing the assay on environmental DNA (eDNA ) samples collected from two lakes, one containing A. gracile and one without the species. Categories: Data; Tags: Aquatic Biology, Genetics, Pacific Northwest, USGS Science Data Catalog (SDC), amphibians, All tags... biota, environmental DNA, Fewer tags Status and trends of adult Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) sucker populations in Upper Klamath Lake, Oregon, 2023 Data were collected as part of a long-term capture-recapture program to assess the population dynamics of two long-lived, federally endangered catostomids in Upper Klamath Lake, Oregon. Lost River suckers (LRS; Deltistes luxatus) and shortnose suckers (SNS; Chasmistes brevirostris) have been captured and tagged with passive integrated transponder (PIT) tags during their spawning migrations in each year since 1995. Cormack-Jolly-Seber (CJS) open population capture-recapture models were used to estimate annual survival probabilities, and a reverse-time analog of the CJS model was used to estimate recruitment of new individuals into the spawning population. In addition, data on the size composition of captured fish... Categories: Data; Tags: Aquatic Biology, USGS Science Data Catalog (SDC), Upper Klamath Lake, biota, demographic rates, All tags... ecology, endangered species, suckers, Fewer tags Survey of viral hemorrhagic septicemia virus in Pacific herring throughout the North Pacific Ocean Throughout a 20-year biosurveillance period, viral hemorrhagic septicemia virus was isolated in low titers from only 6 / 7,355 opportunistically sampled adult Pacific herring, reflecting the typical endemic phase of the disease when the virus persists covertly. However, more focused surveillance efforts identified the presence of disease hot spots occurring among juvenile life history stages from certain nearshore habitats. These outbreaks sometimes recurred annually in the same temporal and spatial patterns and were characterized by infection prevalence as high as 96%. Longitudinal sampling indicated that some epizootics were relatively transient, represented by positive samples on a single sampling date, and others... Categories: Data; Tags: Cook Inlet, Ecology, Ketchican, Prince William Sound, Puget Sound, All tags... Sitka Sound, USGS Science Data Catalog (SDC), Wildlife Disease, viruses, Fewer tags Data collected in 2008-2014 to assess nearshore subtidal community responses to increased sediment load during removal of the Elwha River dams, Washington State, USA Data are time series of substrate grain size, remotely sensed water column turbidity, and measures of abundance (e.g., density, percent cover) of the nearshore subtidal (3-17 m depth) benthic community (vegetation, invertebrates, and fish) collected before (2008-2011) and during dam removal (2012-2014). Categories: Data; Tags: Aquatic Biology, Benthos, Botany, Clallam County, Ecology, All tags... Elwha River, Geomorphology, Habitat alteration, Land Use Change, Marine Geology, Marine nearshore subtidal, Remote Sensing, Species diversity, Strait of Juan de Fuca, USGS Science Data Catalog (SDC), Water Quality, Fewer tags Upper Skagit River intrinsic potential results We assessed habitat suitability for salmonids across selected tributaries upstream from three hydroelectric dams on the upper Skagit River in Whatcom County, northern Washington. We used NetMap, a commercial toolset within the ArcMap geographic information system (GIS), to analyze stream attributes based upon a synthetic stream channel network derived from digital elevation models. The GIS-derived stream attributes—including gradient, bankfull width, valley width index, elevation, and stream flow—allowed us to examine the spatial distribution and relative quality of spawning and rearing habitat for salmonids based on existing intrinsic potential (IP) models. As a first step, we created maps of potential anadromous... Categories: Data; Tags: Ecology, North Cascades National Park, USGS Science Data Catalog (SDC), biota, habitat suitability indices Spatial and temporal surveys of salmon eDNA in Seattle urban creeks, Washington, 2018 - 2020 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. Categories: Data; Tags: Aquatic Biology, Ecology, Genetics, Lake Washington, Seattle, All tags... USGS Science Data Catalog (SDC), environment, environmental DNA, fish, migratory species, salmon, urban streams, Fewer tags Laboratory challenge of Pacific herring Clupea pallasii to Vibrio anguillarum and V. ordallii Controlled waterborne exposures of Pacific herring (Clupea pallasii) to Vibrio anguillarum and V. ordalii failed to result in overt signs of disease or mortality from vibriosis. Cumulative mortalities among Vibrio - exposed Pacific herring (3.3 - 5.0%) were similar to those of saline-exposed negative controls (10%) and significantly less (P < 0.001) than those of Vibrio - exposed Chinook salmon (60 - 97%), a known susceptible species. Gross signs of disease did not occur on any dead or surviving Pacific herring; however, exposed Chinook salmon demonstrated classic gross signs of vibriosis. The results indicate that early reports of presumed vibriosis in Pacific herring during the 1950’s were likely misdiagnosed... Categories: Data; Tags: Ecology, USGS Science Data Catalog (SDC), Wildlife Disease, bacteria, biota, All tags... fish, Fewer tags Information tables associated with a risk assessment for bull trout introduction into Sullivan Lake, northeastern, Washington including population donor sources and resident species, April 2021 Introduction and translocation programs require thoughtful planning to increase the likelihood of success and to understand the benefits, risks, and constraints of such programs. A risk assessment was completed for bull trout introduction into the Sullivan Lake and Harvey Creek watershed, northeastern Washington. The risk assessment was designed to evaluate potential risks to resident fish species, to bull trout introduced into Sullivan Lake, and to bull trout donor source populations. The risk assessment describes the potential risks associated with pathogens, genetics, and ecological interactions. Literature reviews were completed for fish species composition and abundance in Sullivan Lake watershed to assess... Categories: Data; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: Aquatic Biology, British Columbia, Ecology, Genetics, Idaho, All tags... Montana, USGS Science Data Catalog (SDC), Washington, Fewer tags Environmental DNA (eDNA) is an Effective Tool to Track Recolonizing Migratory Fish Following Large-Scale Dam Removal, field data 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. Categories: Data; Tags: Aquatic Biology, Charr, Dam Removal, Ecology, Elwha River, All tags... Elwha River, Genetics, Salmon, USGS Science Data Catalog (SDC), biota, environmental DNA, Fewer tags Disruption of Francisella noatunensis orientalis pdpA gene results in virulence attenuation and protection in zebrafish Several Francisella spp. including F. noatunensis are regarded as important emerging pathogens of wild and farmed fish. However, very few studies have investigated the virulence factors that allow these bacterial species to be pathogenic in fish. The Francisella Pathogenicity Island (FPI) is a well-described, gene-dense region encoding major virulence factors for the genus Francisella. PdpA is a member of the pathogenicity determining protein genes encoded by the FPI that are implicated in the ability of the mammalian pathogen, F. tularensis, to escape and replicate in infected host cells. Using a sacB suicide approach, we generated pdpA knockouts to address the role of PdpA as a virulence factor for F. noatunensis.... Categories: Data; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: Aquatic Biology, USGS Science Data Catalog (SDC), Water Quality, Water Resources, Wildlife Biology, All tags... Wildlife Disease, Fewer tags USGS Dam Removal Science Database v4.0 This database is the result of an extensive literature search aimed at identifying documents relevant to the emerging field of dam removal science. In total the database contains 296 citations that contain empirical monitoring information associated with 207 different dam removals across the United States and abroad. Data includes publications through 2020 and supplemented with the U.S. Army Corps of Engineers National Inventory of Dams database, U.S. Geological Survey National Water Information System and aerial photos to estimate locations when coordinates were not provided. Publications were located using the Web of Science, Google Scholar, and Clearinghouse for Dam Removal Information. Categories: Data; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: Australia, Austria, Canada, Connectivity, Dam Removal, All tags... Ecology, Ecosystems, Energy Resources, Environmental Health, Geomorphology, Hydrologic alteration, Japan, Korea, Land Use Change, Lentic, Lotic, Meta-Analysis, NFHP Cooperator, NoVisual, Norway, Spain, Spatial Data, Sweden, Taiwan, USGS Science Data Catalog (SDC), United States, Wales, Water, Water Quality, Water Resources, Wildlife Biology, environment, inlandWaters, Fewer tags Spatial and temporal survey of waterborne myxozoan parasites in the Lake Sammamish watershed, Washington, from 2019 - 2020 There is a fundamental knowledge gap on the distribution, prevalence, intensity, and ecology of salmonid myxozoan parasites in the Lake Sammamish watershed, Washington. To address this knowledge gap, we tested water samples for Ceratonova shasta, Parvicapsula minibicornis and Tetracapsuloides bryosalmonae DNA from 84 sites distributed throughout the Lake Sammamish watershed in fall 2019 and 74 sites in spring 2020. Our surveillance identified zones with high waterborne parasite loads and provides a proof of concept for this approach that could be expanded throughout the larger Lake Washington watershed. Categories: Data; Tags: Aquatic Biology, Ceratonova shasta, Ecology, Parvicapsula minibicornis, Puget Sound, All tags... Tetracapsuloides bryosalmonae, USGS Science Data Catalog (SDC), Washington, Wildlife Disease, biota, environment, fishes, inlandWaters, parasites, Fewer tags Survival and viral load of chinook salmon, sockeye salmon, and steelhead trout exposed to 4 genogroups of infectious hematopoietic necrosis virus (IHNV) Theory of the evolution of pathogen specialization suggests that a specialist pathogen gains high fitness in one host, but this comes with fitness loss in other hosts. By contrast, a generalist pathogen does not achieve high fitness in any host, but gains ecological fitness by exploiting different hosts, and has higher fitness than specialists in non-specialized hosts. As a result, specialist pathogens are predicted to have greater variation in fitness across hosts, and generalists would have lower fitness variation across hosts. We test these hypotheses by measuring pathogen replicative fitness as within-host viral loads from the onset of infection to the beginning of virus clearance, using the rhabdovirus infectious... Categories: Data; Tags: Aquatic Biology, Ecology, Pacific Northwest, RNA viruses, USGS Science Data Catalog (SDC), All tags... Wildlife Disease, farming, generalism, pathogen, replication, salmonids, specialization, tradeoffs, viral load, Fewer tags Data from 2022 Mark-Recapture Analysis on Water and Endangered Fish in the Klamath River Basin: Do Upper Klamath Surface Elevation and Water Quality Affect Adult Lost River and Shortnose Sucker survival? The data provided were used in a mark-recapture analysis conducted in 2022. Environmental covariates included water quality and Upper Klamath Lake surface elevation. Raw data were downloaded from the USGS Oregon Water Science Center for multiple sampling sites (422622122004000_MDNL_2021-1-14.csv, 422622122004003_MDNU_2021-1-14.csv, 422042121513100_RPT_2021-1-14.csv, 422719121571400_WMR_2021-1-14.csv, MDNL_WQ2_Ammonia_2021-2-3.csv, WMR_WQ2_Ammonia_2021-2-3.csv, Elevation_2021-1-19.csv) and were formatted for use in mark-recapture models. A Program R script (Covariate_Cleaning.R) formats data and then writes multiple csv files with annual environmental covariates for use in subsequent mark-recapture models. Annual... Categories: Data; Tags: Aquatic Biology, Ecology, Klamath County, Limnology, Long-term ecological monitoring, All tags... Oregon, USGS Science Data Catalog (SDC), Water Quality, Water Resources, aquatic biology, endangered species, lake, native species, population dynamics, Fewer tags Detection of invasive aquatic plants Myriophyllum spicatum and Egeria densa in lakes using eDNA, field and mesocosm data We conducted a study to test the factors related to detectability of two invasive aquatic plants (Egeria densa and Myriophyllym spicatum) using environmental DNA (eDNA), over extended periods of time, and specifically examined how plant growth stage and abundance relates to eDNA detection in semi-natural and natural conditions. This dataset is from sampling performed in summer of 2018 in lakes with varying species abundances, and a subset of lakes were re-sampled to test temporal variability in detection. Categories: Data; Tags: Aquatic Biology, Downloadable Data, Ecology, Egeria densa, Myriophyllym spicatum, All tags... USGS Science Data Catalog (SDC), Washington State, biota, eDNA, environment, environmental DNA, invasive species; information management, non-native species, qPCR, Fewer tags Tidal flow dynamics at Sutter and Steamboat Sloughs in the Sacramento-San Joaquin Delta, CA in 2014 The video shows a short animation of river flow dynamics (flow velocity vectors) over multiple tidal cycles. Tags: Aquatic Biology, Hydrology, Sacramento-San Joaquin Delta, USGS Science Data Catalog (SDC), stream-gage measurement Distribution and seasonal differences in Pacific Lamprey and Lampetra spp eDNA across 18 Puget Sound watersheds, 2014 and 2015 These data contain all the raw results needed to support the conclusions for the final product. These data are water sampling locations (latitude and longitude), date of water sampling, quantitative PCR values for each water sample, and stream flow at USGS stream gauging stations on sampling day. Categories: Data; Tags: Aquatic Biology, Ecology, Genetics, Lamprey, Puget Sound, WA, All tags... USGS Science Data Catalog (SDC), environmental DNA, Fewer tags Data from 2018 Experiment on Effects of Temperature on Survival and Growth of Juvenile Lost River Suckers (Deltistes luxatus) naturally exposed to Ichthyobodo spp Data included in this data set are for an experiment conducted in 2018. Data were collected on survival, growth, food consumption, and Ichthyobodo copy numbers of Lost River suckers exposed to five different temperature groups. There are five levels of data. Temperature data contains 1,178 records and the data file is 35 KB, survival data contains 150 records and the data file is 3 KB, food consumption data contains 499 records and the data file is 10 KB, growth data contains 601 records and the data file is 11 KB, Ichthyobodo data contains 39 records and the data file is 2 KB. The data files can be linked on Group and/or Tank which are unique to each temperature group or individual aquarium tank. Data files are... Tags: Aquatic Biology, Chiloquin Oregon, Ecology, Endangered Species, Parasites, All tags... USGS Science Data Catalog, USGS Science Data Catalog (SDC), Wildlife Disease, endangered species, organism growth and development, parasites, water temperature, Fewer tags Experimental Testing of Endangered Pallid Sturgeon to Viral Hemorrhagic Septicemia Virus Genotype IVb Viral hemorrhagic septicemia virus (VHSV) is an aquatic rhabdovirus causing severe disease in numerous freshwater and saltwater fish species. Initially the virus was been found to cause disease in European fish populations starting around 1938 and was first detected in North America in the late 1980s. Of the four VHSV genotypes (I, II, III, and IV), the North American subtype IVb isolates have a broad host range. To determine whether endangered pallid sturgeon Scaphirhynchus albus, are susceptible to VHSV-IVb infection, juvenile pallid sturgeon and two pallid sturgeon cell lines derived from skin and spleen tissue were tested. Detection of viable virus via a plaque assay and molecular detection of the virus results... Categories: Data; Tags: Pathogen, USGS Science Data Catalog (SDC), Wildlife Disease, animal, aquatic, All tags... biota, environment, Fewer tags Laboratory exposure of Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch) and rainbow trout (O. mykiss) to a Pacific Canadian strain of piscine orthoreovirus genotype one (PRV-1) Piscine orthoreovirus genotype one (PRV-1) is the causative agent of heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar L.). The virus has also been found in Pacific salmonids in western North America, raising concerns about the risk to native salmon and trout. Here, we report the results of laboratory challenges using juvenile Chinook salmon, coho salmon, and rainbow trout injected with tissue homogenates from Atlantic salmon testing positive for PRV-1 or with control material. Fish were sampled at intervals to assess viral RNA transcript levels, hematocrit, erythrocytic inclusions, and histopathology. While PRV-1 replicated to high loads in all species, there was negligible mortality... Categories: Data; Tags: Pacific Northwest, USGS Science Data Catalog (SDC), Wildlife Disease, environment 1 2 3 »