Filters: Tags: environmental DNA (X)
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Resource managers conduct landscape-level monitoring using environmental DNA (eDNA). These managers must contend with imperfect detection in samples and sub-samples (i.e., molecular analyses). This imperfect detection impacts their ability to both detect species and estimate occurrence. Although occurrence (synonymously occupancy) models can estimate these probabilities, most models and guidance for their application do not consider three levels. This simulated dataset assumes sites are occupied (probably psi =1, Z = 1 ) and simulates sample (probability theta, A = 0,1) and subsample (probability p, Y = 0, 1) occurrence probabilies and detections (1)/non-detections (0).
This is the qPCR and loop-mediated isothermal amplification (LAMP) data in support of the article "Validation of a portable eDNA detection kit for invasive carps". There are four types of data contained in five files including: limit of detection analysis for each method (qPCR and LAMP), qPCR analysis and LAMP analysis of eDNA samples collected over time from ponds containing 3 or 33 Grass Carp (Ctenopharyngodon idella) mixed with thousands of baitfish. The standards and controls data collected with the eDNA sample analysis are split into separate files for each method to simplify the statistical analysis of the eDNA sample data.
Categories: Data;
Tags: Genetics,
USGS Science Data Catalog (SDC),
biota,
environmental DNA,
grass carp,
These data contain wind speed (m/sec), wind gust (m/sec) and wind direction measurements collected at 1 min intervals with HOBO microstations supporting Davis® S-WCF-M003 wind speed and direction sensors (Onset Computer Corporation, Bourne, Massachusetts, USA). Microstations and wind sensors were placed at 923 m and 1328 m elevations in the Kahuku Unit of Hawaii Volcanoes National Park to collect wind data in parallel with Passive Environmental Samplers for Ceratocystis lukuohia, C. huliohia, and Austropuccina psidii.
Categories: Data;
Tags: Austropuccinia psidii,
Ceratocystis huliohia,
Ceratocystis lukuohia,
Hawaii,
Ohia Lehua,
These data contain Genbank Accession numbers for DNA amplified and sequenced from a subset of Environmental Samplers that were positive for Ceratocystis lukuohia and Austropuccinia by quantitative PCR (qPCR).
Categories: Data;
Tags: Austropuccinia psidii,
Ceratocystis huliohia,
Ceratocystis lukuohia,
Hawaii,
Ohia Rust,
This data consists of information on the specificity and sensitivity of 4 species specific qPCR assays for the detection of eDNA from 4 species of freshwater mussels, specifically Lampsilis cardium, Lampsilis siliquoidea, Pyganodon grandis, and Anodontoides ferussacianus. The data also contain the results of eDNA sampling in Niobrara River at Niobrara National Scenic River and Agate Fossil Beds National Monument for detection of these 4 species.
The data released are associated with an examination of eDNA from round goby fish (Neogobius melanostomus) in a series of field sample collections (lake nearshore and stream transport) and in vitro laboratory experiments. The round goby was used as a model for our source of eDNA in the field collections and mesocosm experiments. The field samples for lake nearshore (water and sediment) were collected from two Lake Michigan shoreline locations (Portage Lakefront, Portage, Indiana and Washington Park, Michigan City, Indiana) to examine the detectability of eDNA, the influence of sediment on eDNA estimates, and eDNA spatial and temporal resolution. The field samples for stream transport (water) were collected from...
Categories: Data;
Tags: Aquatic Biology,
Brown Ditch,
Ecology,
Genetics,
Indiana Dunes National Park,
Data describe the results of a controlled laboratory mesocosm experiment evaluating the influence of a nitrifier enriched microbial community on silver carp (Hypophthalmichthys molitrix) milt eDNA degradation. Parameters described include the concentration results, limit of detection, and limit of quantification of two silver carp specific quantitative PCR assays and water chemistry results of experimental mesocosms.
We tested the sensitivity of a portable, field-based environmental DNA (eDNA) platform relative to widely used lab-based eDNA approaches for detecting invasive northern pike (Esox lucius) in eight lakes on Alaska’s Kenai Peninsula. Raw data reported in this dataset report detect/non-detect data for technical replicates of water samples.
Categories: Data;
Tags: Alaska,
South Central Alaska,
USGS Science Data Catalog (SDC),
aquatic biology,
biota,
We used field surveys to compare coarse filter-large water volume samples (hereafter large volume filter samples) vs. fine filter-small water volume samples (hereafter small volume filter samples) for detection and quantification of bull trout (Salvelinus confluentis). We collected eDNA water samples in 2016 from three long-term fish monitoring sites in tributary streams (~ 2nd order) in the Flathead River, MT with low densities (less than 1 fish per 100 m2) of juvenile bull trout We report the quantity of bull trout DNA detected.
Data describe designed environmental DNA (eDNA) experiments for the estimation of eDNA shedding rates for the spectaclecase (Cumberlandia monodonta) and mucket (Actinonaias ligamentina) from water samples collected in the laboratory at different water temperatures. 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 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 particle sizes of polyethylene spheres that were...
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 compared our two new samplers to Rotorod® samplers using Xyleborus spp. boring dust (frass) known to contain fungi responsible for Rapid ʽŌhiʽa Death. The comparison was done in a large outdoor field cage to determine relative effectiveness of the three samplers for capturing windblown boring dust....
Categories: Data;
Tags: Ceratocystis,
Environmental DNA,
Environmental DNA,
Environmental Sampler,
Environmental Sampler,
These data contain sample information and locality and quantitative polymerase chain reaction (qPCR) results from extraction and testing of individual tape strips within Passive Environmental Samplers (PES). Samplers were placed at 5 locations on Hawaii Island between 2016 and 2017.
Categories: Data;
Tags: Austropuccina psidii,
Ceratocystis huliohia,
Ceratocystis lukuohia,
Hawaii,
Ohia Lehua,
Community composition data from multi-pass electrofishing surveys for assessing fish populations in headwater streams of the Adirondack Mountains, New York, USA. Each row represents one individual fish. This spreadsheet contains 11 columns. The first 7 columns describe the data (year collected, local site ID, stream name, latitude, longitude, USGS site number, and electrofishing pass number) and the remaining 4 columns describe each individual fish (common name, scientific name, total length (mm) and weight (g)). These data support the following publication: Baldigo, B.P., Sporn, L.A., George, S.D., and Ball, Jacob, 2017. Efficacy of environmental DNA to detect and quantify Brook Trout Salvelinus fontinalis, populations...
Categories: Data;
Types: ArcGIS REST Map Service,
ArcGIS Service Definition,
Citation,
Downloadable,
Map Service;
Tags: Adirondack State Park,
Adirondack streams,
Adirondacks,
Aquatic Biology,
DNA,
These data were collected in May, August, and October in west central Colorado from a Bureau of Land Management wild horse herd management area (HMA). Samples were already on the ground, not fresh from the horse. The Diet dataset includes proportion of plant species found in fecal samples using two different lab techniques -- plant DNA bar-coding,and microhistology. Results of both methods to determine diet are in the same spreadsheet. The dung aging dataset consists of samples of different known ages of feces and their amplification results; 8 markers were amplified and data shown in each column indicate whether that marker loci amplified or not. Germination data showed which plant species germinated from fecal...
Categories: Data;
Tags: DNA sequencing,
Fecal DNA,
Little Book Cliffs Herd Management Area,
USGS Science Data Catalog (SDC),
biota,
These data describe microbiological analyses performed on groundwater samples from domestic drinking water supply collected from 42 groundwater wells in the Central Valley of California. Samples were collected between January 2014 and April 2014 for the Groundwater Ambient Monitoring and Assessment (GAMA) program priority basin assessment of the Madera, Chowchilla, and Kings (MACK) groundwater sub-basins’ shallow aquifers. A total of 75 wells were sampled for the MACK study unit between August 2013 and April 2014. Samples for this dataset were vacuum filtered and plated on MI and mEI agars prior to incubation to promote colony growth. Colonies were tallied by their species into columns for various fecal indicator...
Categories: Data;
Tags: California,
Fresno,
GAMA,
Groundwater Ambient Monitoring and Assessment Program,
Kings,
A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes Proliferative Kidney Disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. We present data that was used to determine assay sensitivity, specificity and to define the limits of detection and quantification.
Categories: Data;
Types: Citation;
Tags: East Gallatin River,
Montana,
Sypes Canyon Creek,
Tetracapsuloides bryosalmonae,
Yellowstone River,
Environmental DNA results for water samples collected at USGS streamgages in the Columbia and Colorado river basins. Water samples were collected by USGS hydrologic technicians May - September 2018 and analyzed for presence of kokanee and yellow perch DNA. In this dataset, we report results and applicable covariates associated with each streamgage location. This is version 1.1 of this data release. The Kokanee_Perch_eDNA data and metadata files have been revised to correct for improper attribution of 16 samples. For access to previous versions, please contact the Point of Contact identified on this page.
Environmental DNA detection results from samples collected using autonomous water sampling robots and manual approaches. Samples were collected in the Upper Yellowstone River (Montana) and Upper Snake River (Idaho/Wyoming) in 2018 and 2019. Samples were tested for the DNA of the following species: the waterborne protozoa Naegleria spp., the fish pathogen Tetracapsuloides bryosalmonae, Scomber japonicas (mackerel fish), kokanee salmon (Oncorhynchus nerka) and dreissenid mussel (Dreissena spp.).
Categories: Data;
Tags: Palisades Dam,
USGS Science Data Catalog (SDC),
Upper Snake,
Upper Yellowstone,
Yellowstone National Park North,
Ichthyoplankton tows samples collected from Truman reservoir tributaries evaluated for eDNA. Data also includes hydrologic and water quality parameters and morphology of grass carp eggs.
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