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Filters: Tags: environmental DNA (X) > partyWithName: U.S. Geological Survey - ScienceBase (X) > partyWithName: Katy E Klymus (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.
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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.
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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
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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.
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Data describe specificity and sensitivity testing for the L.sil2 assay. This assay is used to amplify eDNA from the freshwater mussel Lampsilis siliquoidea.
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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.
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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...
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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.
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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.
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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.
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Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the mucket (Actinonaias ligamentina) from water samples collected in the laboratory. Samples were collected from experiments performed from November 01, 2019 to November 15, 2019 at the USGS Columbia Environmental Research Center, Missouri
Data describe a designed environmental DNA (eDNA) survey for the detection of oyster mussel (Epioblasma capsaeformis) 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 oyster mussel DNA. Samples were collected from sites on the Clinch River, Tennessee from 2019 to 2021
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Data describe a designed environmental DNA (eDNA) experiment for the estimation of eDNA degradation rates for the spectaclecase (Cumberlandia monodonta) from water samples collected in the laboratory. Parameters described include laboratory collected water samples that were tested to estimate concentration of spectaclecase DNA and associated quality assurance data. Samples were collected from experiments performed from May 17, 2021 to May 30, 2021 at the USGS Columbia Environmental Research Center, Missouri
    map background search result map search result map Metabarcoding data from freshwater mussel eDNA collected in Clinch River, Virginia 2017 Water chemistry and molecular eDNA data observed in experimental laboratory mesocosms exposed to different nitrogen amendments in the presence or absence of a nitrifier enriched microbial community Environmental DNA (eDNA) Metabarcoding assessment of dead-end hollow fiber ultrafiltration (D-HFUF) and polyethylstyrene (PES) filters filtration methods on detection of freshwater mussel eDNA from Flint River and Spring Creek, Georgia and Big Piney River, Missouri Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Tennessee (2019 to 2021) Degradation of Cumberlandia monodonta environmental DNA over time in laboratory conditions using the C.monCOI assay Development and testing of a qPCR assay for Lampsilis siliquoidea eDNA Environmental DNA shedding rates in laboratory conditions for Cumberlandia monodonta, Actinonaias ligamentina, and Lampsilis siliquoidea. Biomass experiments with Cumberlandia monodonta, Actinonaias ligamentina, and Lampsilis siliquoidea Temperature experiments with Actinonaias ligamentina and Cumberlandia monodonta Food availability experiments with Actinonaias ligamentina and Lampsilis siliquoidea Laboratory estimates of eDNA degradation rates for Actinonaias ligamentina eDNA Development, testing and use of four species-specific qPCR assays for freshwater mussel eDNA detection in the Niobrara River Water chemistry and molecular eDNA data observed in experimental laboratory mesocosms exposed to different nitrogen amendments in the presence or absence of a nitrifier enriched microbial community Degradation of Cumberlandia monodonta environmental DNA over time in laboratory conditions using the C.monCOI assay Development and testing of a qPCR assay for Lampsilis siliquoidea eDNA Environmental DNA shedding rates in laboratory conditions for Cumberlandia monodonta, Actinonaias ligamentina, and Lampsilis siliquoidea. Biomass experiments with Cumberlandia monodonta, Actinonaias ligamentina, and Lampsilis siliquoidea Temperature experiments with Actinonaias ligamentina and Cumberlandia monodonta Food availability experiments with Actinonaias ligamentina and Lampsilis siliquoidea Laboratory estimates of eDNA degradation rates for Actinonaias ligamentina eDNA Development, testing and use of four species-specific qPCR assays for freshwater mussel eDNA detection in the Niobrara River Metabarcoding data from freshwater mussel eDNA collected in Clinch River, Virginia 2017 Data on the detection of Epioblasma capsaeformis using a designed environmental DNA (eDNA) survey upstream and downstream of known populations in the Clinch River, Tennessee (2019 to 2021) Environmental DNA (eDNA) Metabarcoding assessment of dead-end hollow fiber ultrafiltration (D-HFUF) and polyethylstyrene (PES) filters filtration methods on detection of freshwater mussel eDNA from Flint River and Spring Creek, Georgia and Big Piney River, Missouri