Filters: Tags: environmental DNA (X) > partyWithName: U.S. Geological Survey (X)
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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,
We designed two new samplers for monitoring airborne particulates, including fungal and fern spores and plant pollen, that rely on natural wind currents (Passive Environmental Sampler) or a battery operated fan (Active Environmental Sampler). Both samplers are modeled after commercial devices such as the Rotorod® and the Burkard samplers, but are more economical and require less maintenance than commercial devices. We conducted wind tunnel comparisons of our two new samplers to Rotorod® samplers using synthetic polyethylene spheres (12 - 160 µm in diameter) to compare numbers and size range of particulates that are captured by the samplers. This dataset contains raw numbers of polyethylene spheres that were captured...
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...
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.
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,
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.
Rapid ʽŌhiʽa Death (ROD) currently threatens ōhiʽa lehua (Metrosideros polymorpha) on Hawaiʽi Island. First identified in Puna in 2014, the disease has now spread island wide. Besides direct sampling of trees, environmental sampling could serve as an easier and broader strategy to detect Ceratocystis spp., the fungi causing ROD. Environmental sampling could also help monitor the effect of felling ROD infected trees. We developed Passive and Active Environmental Samplers and deployed them at a property in Puna, where both C. lukuohia, and C. huliohia had been detected, and where the land owner practiced the management method of felling infected trees. We set up 2 Active Environmental Samplers (modified mosquito traps...
Categories: Data;
Tags: Ceratocystis,
Environmental DNA,
Environmental Sampler,
Hawaiii,
Management,
Water samples from the Platte River were collected and analyzed for environmental DNA (eDNA). The U.S. Geological Survey (USGS) Nebraska Water Science Center (NEWSC) collected samples monthly from November 2019 to September 2022 at the Platte River near Ashland, Nebraska (USGS: 06801000). The USGS, in cooperation with the City of Lincoln, collected these samples. Water from the Platte River was collected as a series of weighted bottle subsamples that were taken from equal width increments across the river and composited into a sterilized 1-liter bottle. An aliquot of this composited sample was extracted using a sterile syringe and then filtered by the USGS NEWSC staff using filters provided by Jonah Ventures. These...
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),
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.
Field estimates of the abundance of rainbow trout in Washington and British Columbia were collected in concert with environmental DNA samples (eDNA) to evaluate if eDNA copy numbers correlated with abundance of trout. In addition, stream habitat data including channel units (pools, riffles), substrate, large woody debris, among others, were collected at sites.
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....
Environmental DNA (eDNA) detection tools are becoming increasingly popular for documenting occurrence and distribution of native and invasive species. These tools can allow early detection of new diseases and invasive species and provide critical information for land management. We designed two new samplers for monitoring airborne particulates, including fungal and fern spores and plant pollen, that rely on natural wind currents (Passive Environmental Sampler) or a battery operated fan (Active Environmental Sampler). This dataset contains results of an experiment that was designed to determine probability of detecting known numbers of Ceratocystis lukuohia spores on individual slides in these samplers.
Categories: Data;
Tags: Ceratocystis,
Environmental DNA,
Environmental Sampler,
Hawaiii,
Metrosideros polymorpha,
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,
Field estimates of the abundance of two trout species (bull trout and westslope cutthroat trout) in Montana and rainbow trout in Washington and British Columbia were collected in concert with environmental DNA samples (eDNA) to evaluate if eDNA copy numbers correlated with abundance of trout. In addition, stream habitat data including channel units (pools, riffles), substrate, large woody debris, among others, were collected at sites.
The dataset includes measurements of stream habitat, fish abundance of westslope cutthroat trout and bull trout, and species-specific measures of environmental DNA (eDNA) from within the water. The data covers multiple streams in western Montana.
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