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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,
Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore eDNA decay in waste materials and reproductive cells obtained...
Categories: Data;
Types: Citation;
Tags: Aquatic Biology,
Ecology,
Environmental Health,
Genetics,
Missouri,
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,
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove) Japan, Safety Sound, Izembek Lagoon, Port Moller, Chignik Lagoon, and Frederick Sound, Alaska and cloacal swabs from waterfowl hunted near Cold Bay Alaska. Replicate samples and multiple sampling dates of the same location were included. Highly conserved primers which could differentiate species of interest were developed for four...
Categories: Data;
Tags: Alaska,
Animals/Vertebrates,
Aquatic Biology,
Aquatic ecosystems,
Biological informatics,
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
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,
The Great Plains Landscape Conservation Cooperative (GPLCC, https://www.fws.gov/science/catalog) is a partnership that provides applied science and decision support tools to assist natural resource managers conserve plants, fish and wildlife in the mid- and short-grass prairie of the southern Great Plains. It is part of a national network of public-private partnerships — known as Landscape Conservation Cooperatives (LCCs, http://www.fws.gov/science/shc/lcc.html) — that work collaboratively across jurisdictions and political boundaries to leverage resources and share science capacity. The Great Plains LCC identifies science priorities for the region and helps foster science that addresses these priorities to support...
Categories: Data;
Types: Downloadable,
GeoTIFF,
Map Service,
Raster;
Tags: Digital Elevation Model,
EDNA,
GPLCC,
Great Plains Landscape Conservation Cooperative,
Hydrologic Derivative,
The Great Plains Landscape Conservation Cooperative (GPLCC, https://www.fws.gov/science/catalog) is a partnership that provides applied science and decision support tools to assist natural resource managers conserve plants, fish and wildlife in the mid- and short-grass prairie of the southern Great Plains. It is part of a national network of public-private partnerships — known as Landscape Conservation Cooperatives (LCCs, http://www.fws.gov/science/shc/lcc.html) — that work collaboratively across jurisdictions and political boundaries to leverage resources and share science capacity. The Great Plains LCC identifies science priorities for the region and helps foster science that addresses these priorities to support...
Categories: Data;
Types: Downloadable,
GeoTIFF,
Map Service,
Raster;
Tags: Aspect,
Colorado,
Downslope Direction,
EDNA,
GPLCC,
Eggs were collected in the Upper Mississippi main stem (Pool 9 and Pool 11) during the summer of 2013. Using previously published morphological characteristics, eggs were positively identified as belonging to an invasive Asian carp genus. A subsample of these eggs was subsequently analyzed using molecular methods to determine species identity. Genetic identification of a total of 41 eggs was attempted using the cytochrome c oxidase 1 (COI) gene. Due to the preservation technique used (formalin) and resulting DNA degradation, sequences from only 17 individuals could be recovered. In all cases, non-carp cyprinids were identified as the most likely species identity (usually a Notropis spp.). In previously published...
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Mississippi River,
USGS Science Data Catalog (SDC),
eDNA,
environmental DNA
This data release includes metadata and tabular data that documents lab and field trials testing the efficacy of carbon dioxide (CO2) gas diffused into water to manage invasive fish in anchialine pools. The data release also includes information documenting sensitivity, specificity, and accuracy of quantitative polymerase chain reaction (qPCR) assays to detect environmental DNA (eDNA) from tilapia (Oreochromis mosambicus), western mosquitofish (Gambusia affinis) and guppies (Poecilia reticulata). In total there are 11 datasets, 9 describing lab trials and 2 describing field trials. Lab data include 1) initial water conditions during pilot study, 2) behavioral response of fish to CO2 during pilot study, 3) survival...
This file contains one of many raster grids of the Elevation Derivatives for National Applications (EDNA), a multi-layered database that provides systematic and consistent topographically-derived hydrologic derivatives. The slope grid was generated from the filled DEM using the "slope" function. The grid was created with the degree, not percent, slope parameter.
Categories: Data;
Types: Downloadable;
Tags: EDNA,
Federal Government,
Hydrologic Derivative,
LANDFIRE,
Raster digital data,
The data sets contains hierarchical taxonomic identification information for DNA sequences detected in water samples from 5 locations.
Categories: Data;
Tags: Aquatic Biology,
Decision-Making Support and Tools,
Ecology,
Mammals,
Nevada,
This data contains environmental DNA (eDNA) sample assay results that were collected from water samples taken from a tank housing Asian carp and placed either on ice or at room temperature. At both treatment temperatures, water samples were left untreated or were treated with an ethanol and sodium acetate solution (EtOH-NaAc). This was done to evaluate an ethanol and sodium acetate solution to maintain the integrity of the DNA samples for the time between collection and lab testing. Every day for 6 days following collection, a subset of the samples was removed from each treatment and DNA was extracted and nuclear and mitochondrial markers were assayed with qPCR. Results showed comparable persistence of DNA between...
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,
Detection of environmental DNA (eDNA) has become a commonly used surveillance method for threatened or invasive vertebrates in both aquatic and terrestrial environments. However, use of eDNA methodologies for the detection of aquatic invertebrates (e.g., crayfish and insects) has been limited. Environmental DNA protocols can be especially useful for endangered invertebrates such as the Hine’s emerald dragonfly (Somatochlora hineana) where conservation efforts have been greatly hindered by the training, time, overall costs, and environmental impacts associated with conducting surveys in the calcareous fens occupied by this species. An essential step in developing such a protocol is to evaluate the dynamics of eDNA...
Categories: Data;
Tags: Aquatic Biology,
Door County, Wisconsin,
HED,
Hine's Emerald Dragonfly,
USGS Science Data Catalog (SDC),
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,
This file contains one of many raster grids of the Elevation Derivatives for National Applications (EDNA), a multi-layered database that provides systematic and consistent topographically-derived hydrologic derivatives. The filled DEM grid was created from the original elevation data by filling all of the depressions, or sinks, in the original DEM. To create this grid, an algorithm was used to loacted and fill all depressions or sinks where there was no flow from pixel to pixel. During this process, efforts were made to maintain natural sink features.
Categories: Data;
Types: Downloadable;
Tags: Digital Elevation Model,
EDNA,
Federal Government,
Filled DEM,
Hydrologic Derivative,
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