Filters: partyWithName: Christopher M Merkes (X) > partyWithName: U.S. Geological Survey - ScienceBase (X)
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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,
Invasive species may vary in their seasonal distribution and abundance due to environmental conditions such as precipitation and temperature. Bigheaded carps, which include silver and bighead carp, are one such taxon of invasive species that appear to change habitats seasonally. Seasonal changes in bigheaded carp distribution may occur because of hydrological changes, water temperature changes, and spawning activities. Monitoring this seasonal dispersal and migration is important for management to control the population size and spread of the species. We examined if environmental DNA (eDNA) approaches could detect seasonal changes in the occurrence of DNA in water samples and used these approaches to calculate the...
Categories: Data;
Types: Citation,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Americus,
French Post,
Indiana,
Mascouten,
Occupancy modeling,
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
This dataset includes information from ichthyoplankton sampling for silver carp and bighead carp collected from three main reaches in the Upper Mississippi River Basin, including the La Grange, Peoria, Starved Rock, and Marseilles reaches of the Illinois River, Pool 20 of Mississippi River, and the St. Croix River. Data include the number of bigheaded carp eggs and larvae identified using traditional manual sorting techniques, and genetic data derived from quantitative PCR (qPCR) and 4 bigheaded carp markers (SCTM4/5 and BHTM1/2) that were used to identify the amount of DNA in ichthyoplankton tow samples. These data provide information for natural resource agencies and managers who could use this qPCR screening...
Categories: Data;
Tags: Hypophthalmichthys,
Illinois,
Illinois River, USA,
Iowa,
Midwest Region, USA,
This script is designed to analyze qPCR data for many replicates of known concentration DNA standards and determine the limit of detection (LoD) and limit of quantification (LoQ) for use in environmental DNA applications. It is written in the hopes that users with even limited knowledge of R will be able to successfully use the code to analyze their own data in the same way as other eDNA researchers to get similar results and automatically generate plots to visualize the data. The code has 5 lines for user input and requires a few simple restrictions on the input data, but after that the user should be able to run the code without any further coding or interventions. No R programming ability is required to run this...
Categories: Data
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 code supports the manuscript "Reporting the limits of detection (LOD) and quantification (LOQ) for environmental DNA assays". The code analyzes outputs generated by another more generic code to analyze raw qPCR data for LOD and LOQ. This code requires the generic LOD / LOQ calculator script to read in and prepare the data, with additional script runs as described in comments within this code. We wrote this code to specifically analyze our data and generate the figures for the above-mentioned manuscript, however it could be adaptped by a savvy programmer to run similar analyses.
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 environmental DNA data and corresponding water quality data were collected and analyzed by the Fish and Wildlife Service in 2017. The samples were collected from 4 sites in pools 17 and 18 in the Upper Mississippi River on 3 sampling trips. The data was used to study occupancy modeling of eDNA data and determine optimal sampling effort required for reliable detection of invasive Bighead Carp and Silver Carp in streams with similar attributes at the Mississippi River.
Categories: Data;
Tags: Asian carp,
Bighead carp,
Environmental DNA,
Silver carp,
USGS Science Data Catalog (SDC),
This is the mortality and water quality data for 2 efficacy trials of medicated feed for controlling mortality in Walleye (Sander vitreus) due to motile aeromonad infections. Top-coated feed with florfenicol or oxytetracycline or control feed were administered in both trials to fingerling walleye. Daily mortality counts and water quality measurements for dissolved oxygen, pH, temperature are included as csv files.
Categories: Data;
Tags: Aquatic Biology,
MAS,
USGS Science Data Catalog (SDC),
biota,
coolwater finfish,
In 2018 and 2019, a multidisciplinary team from the U.S. Geological Survey (USGS), National Park Service, The Commonwealth Scientific and Industrial Research Organization, Montana State University’s Department of Microbiology and Immunology, and the Teton Conservation District, initiated a study to document the presence or absence of Naegleria fowleri, Giardia, Escherichia coli, and Cryptosporidium at several hot springs in Grand Teton National Park and John D. Rockefeller Jr. Memorial Parkway and Bridger-Teton National Forest, Yellowstone National Park, and Lake Mead National Recreation Area. This data release includes qPCR data from this investigation.
Categories: Data;
Tags: Aquatic Biology,
Arizona,
Arizona Hot Spring,
Astoria Hot Springs,
Blue Point Spring,
Spectaclecase (Margaritifera monodonta) is a federally endangered freshwater mussel species that has experienced a 55% reduction in range (USFWS 2014) and is currently concentrated in three rivers in the Midwest of the United States (Gasconade, Meramec Rivers, MO, and St. Croix River, WI). Its preference for living under large rocks and boulders has limited detection of new populations by traditional survey methods. Environmental DNA technology has been used to detect invasive and rare species, but its use for detection of rare, benthic-dwelling species in large flowing systems has been limited. Here, we propose using environmental DNA to identify presumable sites for discovery of M. monodonta. We designed a M....
Categories: Data;
Tags: Illinois,
Margaritifera monodonta,
Minnesota,
St Croix River,
USGS Science Data Catalog (SDC),
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,
Spreadsheets include data that was used to evaluate the efficacy of dry ice administered under-ice as a tool for reducing the overwinter survival of invasive carps. There are 10 CSV associated with this study
Categories: Data;
Tags: Asian carp,
USGS Science Data Catalog (SDC),
United States,
Winterkill,
biota,
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