Filters: Tags: environmental DNA (X) > partyWithName: Ecosystems (X) > partyWithName: U.S. Geological Survey - ScienceBase (X)
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This data release documents specificity of quantitative polymerase chain reaction (qPCR) assays to detect environmental DNA (eDNA) from tilapia, western mosquito fish and guppies. These assays provide new tools for resource managers to monitor effectiveness of management efforts to remove invasive fish from anchialine pools in Hawaii and to also survey pools for presence and absence of invasive fish. The lab work was conducted during 2019-2022.
Bullseye snakehead, Channa marulius, was first detected in 2000 in the southern Florida town of Tamarac and has been expanding its geographic range. Environmental DNA (eDNA) analysis is a newly-developed technique used to non-invasively detect cryptic or low-density species, or those that are logistically difficult to study. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of target species eDNA. To help delineate bullseye snakehead’s geographic range, we developed and validated a species-specific eDNA assay for both quantitative and droplet digital PCR (ddPCR). We then used ddPCR to assess 16 locations in southeast Florida...
Data from metabarcoding assays to detect a suite of mussel species using mitochondrial DNA regions of the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit (ND1) genes sequences.
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,
This data was collected by the US Fish and Wildlife Service to see if environmental DNA (eDNA) varied across pools and within pools in the Illinois River basin. The data was collected in 2015 from three different habitat types: shoreline, main channel, and bays. The resulting data were then analyzed using an occupancy model.
Categories: Data;
Tags: Illinois,
USGS Science Data Catalog (SDC),
biota,
environment,
environmental DNA,
To evaluate the ability of precipitation-based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well-studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on traditional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predicts eDNA detection. Fish community composition was estimated for seven lakes and two MIssissippi River navigation pools using sequence data from the mitochonrial 12S gene amplified from 10 to...
Positive and negative dreissenid mussel DNA quantitiative PCR results from environmental DNA water samples collected in Montana, Wisconsin and Minnesota to assess if environmental DNA can extend the seasonal window for dreissenid mussel early detection.
Categories: Data;
Tags: Flathead,
Missouri-Marias,
Pepin,
USGS Science Data Catalog (SDC),
Upper Mississippi,
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for the spectaclecase (Cumberlandia monodonta), mucket (Actinonaias ligamentina), and fatmucket (Lampsilis siliquoidea) from water samples collected in the laboratory under differing laboratory conditions. Shedding rates were tested under variable mussel biomass, diet, and temperature. Parameters described include descriptions of laboratory collected water samples that were tested to estimate concentration of spectaclecase, mucket or fatmucket DNA qPCR results, and associated quality assurance measurements.
Categories: Data;
Tags: Columbia Environmental Research Center,
climatologyMeteorologyAtmosphere,
eDNA,
eDNA Shedding rates,
environmental DNA,
Reported here are the metabarcoding read numbers and biomass data assessed from a fish community in a southern Florida pond in Pinecrest Gardens after invasive species eradication and native restocking in 2017 and 2018 in linear regression models. This dataframe contains the number of fish of each species identified, their measured lengths estimated population surface area, and the number of metabarcoding reads (with SD and COV) for each species observed from the sampling date.
Categories: Data;
Tags: Ecology,
Genetics,
Genetics,
Southern Florida,
USGS Science Data Catalog (SDC),
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.
Data included are from a series of field sample collections from Lakes Michigan and Huron, and laboratory mesocosms targeting the round goby fish (Neogobius melanostomus). The round goby is a benthic fish that has heavily invaded four of the five Laurentian Great Lakes. Because it inhabits a variety of substrates, including coastal breakwaters, traditional methods (e.g., trawling, trapping) are inadequate to quantify overall population size. Environmental DNA (eDNA) may be a viable option for improving detection and quantification of the species. Field data include number of round goby caught and associated ambient conditions of the aquatic matrix (temperature, pH, turbidity, conductivity, dissolved oxygen). Mesocosm...
Categories: Data;
Tags: Indiana Dunes National Lakeshore,
Lake Huron,
Lake Michigan,
USGS Science Data Catalog (SDC),
biota,
Real-time PCR results of a round robin evaluation of 5 assays that target dreissenid mussel DNA. Water samples collected from waters with and without dreissenid mussels were analyzed using these five assays in four USGS laboratories. Samples from waters without dreissenid mussels were spiked with known amounts of dreissend DNA.
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.
Biological indicator taxa have long been used for integrative assessments of water quality, particularly benthic invertebrate groups such as arthropods. While standardized protocols have been developed to calculate 'biological index' scores based on the abundances of these taxa, such systems are challenging to implement at large scales due to the sampling effort required, taxonomic expertise needed, and the need for repeated sampling to reliably discriminate sites. Many of the same taxa detected by traditional surveys can also be detected by genetic analysis of environmental DNA (eDNA), potentially allowing for an alternative formulation of biological indexes that might be faster and more economical to produce....
This data set was collected to provide examples and aid in developing a standardized way of determining LOD and LOQ for eDNA assays and has 3 data files. GEDWG_LOD_DATA3.csv is raw qPCR data from multiple labs running multiple standards of known concentration for eDNA assays they regularly use. Comparison-Data.csv is the merged data output from running a generic LOD/LOQ calculator script multiple times with different LOD model settings. The generic LOD/LOQ calculator script is available at: https://github.com/cmerkes/qPCR_LOD_Calc, and details about the multiple settings used are commented in the analysis script available at: https://github.com/cmerkes/LOD_Analysis
U.S. Geological Survey decision analysts and technical experts worked with representatives from the U.S. Bureau of Reclamation, Utah Division of Wildlife Resources, and Central Utah Water Conservancy District to predict the consequences of alternative actions following environmental DNA detections of dreissenid mussel eDNA in Jordanelle Reservor, Utah. This dataset provides the consequence and model inputs for each of the alternative actions under different levels of uncertainty.
Categories: Data;
Tags: Aquatic Biology,
Ecology,
Genetics,
Jordanelle Reservoir,
USGS Science Data Catalog (SDC),
These data include metadata and associated data files associated with the manuscript, "Economical Environmental Sampler Designs for Detecting Airborne Spread of Fungi Responsible for Rapid ʽŌhiʽa Death." These data include a total of 8 datasets used for both controlled and field studies evaluating the use of Active (with battery operated fan) and Passive (dependent on wind) USGS Environmental Samplers on Hawaii Island between 2016-2018. Samplers were operated under controlled laboratory and field conditions with a commercial sampler (Rotorod® Model 20) to compare efficacy in capturing synthetic polyethylene spheres (12 - 160 µm in diameter) and also Xyleborus spp. boring dust (frass) known to contain the fungi responsible...
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for mucket (Actinonaias ligamentina) and fatmucket (Lampsilis siliquoidea) from water samples collected in the laboratory under differing food avilability scenarios. Parameters described include descriptions of laboratory collected water samples that were tested to estimate concentration of spectaclecase, mucket or fatmucket DNA qPCR results, and associated quality assurance measurements.
Categories: Data;
Tags: Columbia Environmental Research Center,
climatologyMeteorologyAtmosphere,
eDNA,
eDNA Shedding rates,
environmental DNA,
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,
eDNA-based spatiotemporal distribution data (occupancy model format) for rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) within the Bruneau-Jarbidge Rivers Wilderness in southern Idaho and northern Nevada, USA. Data also include stream discharge and stream temperature data for each site. All data were collected between October 2015 and September 2016.
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