Filters: Tags: environmental DNA (X)
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This data release documents results of quantitative polymerase chain reaction (qPCR) assays to detect environmental DNA (eDNA) from tilapia, western mosquito fish and guppies in pools with known fish populations and in pre and post-treatment samples from pools that were treated with carbon dioxide gas. 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.
Environmental DNA results for March 2022 smallmouth bass surveillance in the Gardner River, Montana
Categories: Data;
Tags: Aquatic Biology,
Gardner River,
Montana,
Smallmouth Bass,
USGS Science Data Catalog (SDC),
We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicability of the present assays surpass previous methods for detecting T. bryosalmonae DNA from fish tissue and water samples.
Categories: Data;
Types: Citation;
Tags: California,
Idaho,
Montana,
PCR,
Proliferative Kidney Disease,
Tabular amplification data for individual technical replicates of tissue and water samples collected from Glacier National Park in 2020 and amplified with a Lednia tumana species-specific qPCR assay. Reported results include fractional detection rates, mean quantification cycles, and estimated gene copies per reaction.
Categories: Data;
Tags: Aquatic Biology,
Ecology,
Genetics,
Glacier National Park,
USGS Science Data Catalog (SDC),
This dataset has been archived; it has been superseded by version 4.0 (November 2022) which can be found at https://doi.org/10.5066/P9ZCMH8S. The dataset is composed of two tables containing environmental DNA (eDNA) data and site location information from round goby (Neogobius melanostomus) surveys conducted on parts of the Champlain Canal and upper Hudson River in New York during 2022. First posted May 5, 2022, ver. 1.0 Revised June 2022, ver. 2.0 Revised August 2022, ver. 3.0
This data set is associated with an examination of environmental DNA (eDNA) from the invasive round goby (Neogobius melanostomus) in parallel with traditional fish surveys in the Great Lakes. Data resulting from bottom trawling surveys and angler hook and line methods include round goby fish count and biomass at different depths and seasons at multiple sites of Lake Huron and Lake Michigan (trawls), and breakwall locations of Lake Michigan at Portage Lakefront, Portage, Indiana and Washington Park, Michigan City, Indiana (angling). Data from eDNA water samples targeting round goby were analyzed by two molecular methods: droplet digital PCR (ddPCR) and quantitative PCR (qPCR); eDNA copy numbers are presented for...
Environmental DNA (eDNA) water samples were collected at 15 tree islands containing wading bird breeding colonies (order Pelecaniformes) and 15 empty control islands in the central Everglades of Florida in spring of 2017 (April through June) and analyzed for the presence of eDNA from invasive Burmese pythons (Python bivittatus). The Burmese python is now established as a breeding population throughout south Florida, USA. Pythons can consume large quantities of prey and may be a particular threat to wading bird breeding colonies in the Everglades. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis—a genetic tool which detects shed DNA in water...
Categories: Data;
Types: Downloadable,
GeoTIFF,
Map Service,
Raster;
Tags: Aquatic Biology,
Broward,
Everglades,
Genetics,
Miami-Dade,
Data describe a designed environmental DNA (eDNA) survey for the detection of Spectaclecase (Cumberlandia monodonta, also referred to as Margaritifera monodonta) from field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater mussel species tissue samples that were used to test specificity of the assay; and field collected water samples that were tested to detect the presence of Spectaclecase DNA. Samples were collected from sites on the Big Piney River, Missouri from 2020 to 2022.
Categories: Data;
Tags: Big Piney River, Missouri,
USGS Science Data Catalog (SDC),
biota,
environment,
environmental DNA,
Data describe specificity and sensitivity testing for the L.sil2 assay. This assay is used to amplify eDNA from the freshwater mussel Lampsilis siliquoidea.
Categories: Data;
Tags: Aquatic Biology,
Boone County, Missouri,
Columbia Environmental Research Center,
USGS Science Data Catalog (SDC),
biota,
This data release documents sensitivity 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.
U.S. Geological Survey decision analysts and technical experts worked with managers and stakeholders to predict the consequences of alternative actions following environmental DNA detections of invasive Najas minor eDNA in Sebago Lake, Maine, USA. 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,
Sebago Lake,
USGS Science Data Catalog (SDC),
Abstract: Environmental DNA (eDNA) is DNA that has been released by an organism into its environment, such that the DNA can be found in air, water, or soil. In aquatic systems, eDNA has been shown to provide a sampling approach that is more sensitive for detecting target organisms faster, and less expensively than previous approaches. However, eDNA needs to be sampled in a manner that has been tested and found effective and, because single copies of target DNA are detected reliably, rigorous procedures must be designed to avoid sample contamination. Here we provide the details of a sampling protocol designed for detecting fish. This protocol, or very similar prototypes, has been used to collect data reported in...
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: EARTH SCIENCE > LAND SURFACE > LANDSCAPE,
Federal resource managers,
LCC Network Science Catalog,
Report,
State agencies,
Quantitative PCR data from mesocosm experiments and field evaluations comparing coarse filter-large water volume environmental DNA samples vs. fine filter-small water volume environmental DNA samples for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. Mesocosm experiments took place at the US Fish & Wildlife Service's Creston Fish Hatchery in Montana, 2016. Field surveys took place in the Flathead River basin of Montana, 2016.
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.
The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska and analyzed with quantitative PCR.
Categories: Data;
Tags: Alaska,
Aquatic Biology,
USGS Science Data Catalog (SDC),
biota,
environmental DNA
This dataset contains raw sequence data collected from an eDNA metabarcoding project to detect freshwater mussel species across two sites in Georgia (Spring Creek and Flint River) and one drainage in Missouri (Big Piney River). The eDNA samples were collected from each stream using dead-end ultra filtration (D-HFUF) with eDNA extracted from filters. We used two previously published primer sets designed to amplify freshwater mussels, one that amplified the mitochondrial cytochrome c oxidase I (COI) region and one that amplified the NADH dehydrogenase subunit I region, with negative control and mock community samples included. Samples were individually indexed, pooled, and sequenced on an Illumina MiSeq high-throughput...
Columns of data representing Chehalis River tributary, sample reach locations, dates of water sampling, quantitative PCR results, and whether lamprey were sampled by electrofishing in each sample reach. ***Please note that the title of this data release used to be "Environmental DNA surveys for lampreys in Chehalis River tributaries, Washington, from 2015 and 2017," but was updated for version 2.0.
Categories: Data,
Data Release - Revised;
Tags: Chehalis River,
USGS Science Data Catalog (SDC),
biota,
environmental DNA,
lampreys
Data are relative fluorescent units obtained from the FAM channel of a AmpliFire Isothermal Fluorometer (Agdia, Inc., Elkhart, USA) recorded every 10 sec during as isothermal (LAMP) amplification. The isothermal reaction is to detect the Asian fish tapeworm, Schyzocotyle acheilognathi [syn. Bothriocephalus]. Samples (column headers) are described in tabs and include 1) positive control dilution series, 2) DNA Extractions from AFT sensitivity samples, and 3) DNA Extracted from non-AFT specificity controls.
Categories: Data;
Tags: Asian fish tapeworm,
LAMP assay,
USGS National Wildlife Health Center,
USGS Science Data Catalog (SDC),
Wildlife Disease,
Data is a spreadsheet of the number of copies of Zebra Mussel DNA detected and the number of positive detections for Zebra Mussel DNA from water samples collected over 6 different substrates, at 4 depths in 2 lakes. The ash-free dry weight of the mussels at each of the sites is also included for each sampling location.
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Alexandria, MN,
Dreissena polymorpha,
Dreissenid mussels,
Lake Le Homme Dieu, MN,
Maple Lake, MN,
This dataset includes quantifications of bigheaded carp DNA found in water samples collected from the Wabash River along transects at 3 sites over time. The samples were collected at 18 equidistant points in a transect across the river at each site. Samples were collected in 2013 on May 29, 30, 31, June 5, 6, 7, 8, 9, 10, 11, 16, 17, 19, 20, 21, and 22. Quantitative polymerase chain reaction (qPCR) was performed to determine the DNA concentrations in two replicates using the bigheaded carp assay defined in Merkes and others 2014.
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Americus,
Asian carp,
Bigheaded carps,
Environmental DNA,
French Post,
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