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The effects of North American fungi and bacteria on Phragmites australis leaves 2017-2019, with comparisons to the global Phragmites microbiome The data document the results of several microbe bioassays performed by the USGS on Phragmites australis plants, including those performed on mature leaves, seedlings, and dead leaf tissues exploration of the literature to find accounts of microbes associated with Phragmites worldwide. For the bioassays, we prepared 162 pure cultures isolated from Phragmites plants in North America along the east coast, Florida, the Gulf of Mexico, and the Great Lakes area, 125 of which were from a previous study, and 38 represent new collections. The DNA sequences used to identify the 37 new collections are included. Microbes were isolated from plants collected from 2015-2018. We performed assays using both North American plant... Categories: Data; Tags: Africa, Asia, China, DNA sequencing, Ecology, All tags... Europe, Florida, France, Genetics, Germany, Hong Kong, Indiana, Italy, Japan, Louisiana, Maine, Maryland, Michigan, New Jersey, North America, North Carolina, Ohio, Philippines, Poland, Portugal, Rhode Island, Russia, Spain, USGS Science Data Catalog (SDC), United Kingdom, Virginia, bacteria, biota, flowering plants, fungi, pathology, plant and animal testing, systematics and taxonomy, Fewer tags Molecular and distributional data used to investigate misidentifications, population genetic diversity, and spatiotemporal trends in distribution for Pleurobema riddellii to help guide ESA listing decisions We provide genetic and distribution data for the Louisiana Pigtoe, Pleurobema riddellii, to guide decisions related to federal protection for the species under the U.S. Endangered Species Act. Our final dataset includes 125 COI sequences generated as part of our study representing P. riddellii from eight North American river basins. This includes the COI sequence we generated from a museum specimen collected from the Trinity River in the late 1900s, which is the first genetic confirmation of P. riddellii in the Trinity River basin. Also included are sequences from specimens initially identified as Fusconaia cerina (n=3) Fusconaia flava (n=1), Fusconaia sp. (n=5), Pleurobema sintoxia (n=10), and Pustulosa pustulosa... Categories: Data; Tags: Amite River, Aquatic Biology, Arkansas, Calcasieu River, Genetics, All tags... Lake Pontchartrain, Little River, Louisiana, Mississippi, Neches River, Oklahoma, Ouachita River, Pearl River, Sabine River, Saline River, San Jacinto River, Texas, Trinity River, USGS Science Data Catalog (SDC), biota, conservation, endangered species, freshwater mussels, genetics, range extension, species status assessment, Fewer tags Bullseye snakehead environmental DNA data, and associated attributes, collected from southeast Florida, from 2015-2018 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... Categories: Data; Tags: Aquatic Biology, Ecology, Everglades, Genetics, Southern Florida, All tags... USGS Science Data Catalog (SDC), Wildlife Biology, environment, environmental DNA, invasive species, non-invasive monitoring, occupancy estimate, range delimitation, Fewer tags Experimental observations on the decay of environmental DNA from bighead and silver carp-Data 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, All tags... USGS Science Data Catalog (SDC), eDNA, environmental factors, microbial load, pH, water temperature, Fewer tags Genomic Determination of Hoary Bat Population History and Trend Observing and counting bats is extremely difficult. Bats hide during the day, fly in darkness, and most species in the United States (US) become inactive and inaccessible in cryptic hibernation sites for 7-8 months each year. More than 40 different species of bats occur year-round in the US, yet reasonable population estimates exist for very few. Populations of US bats face new and unprecedented threats from white-nose syndrome (WNS) and industrial wind turbines. Like WNS, wind energy development might adversely affect entire populations of bats. Species of bats dying at wind turbines in the greatest numbers rank among the most cryptic, elusive, and poorly understood. Hoary bats (Lasiurus cinereus) compose approximately... Categories: Data, Project; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: EARTH SCIENCE > LAND SURFACE > LANDSCAPE, Hoary bat, Midwest R3 Science Applications, Project, environment, All tags... funded, genetics, genomics, population dynamics, Fewer tags Genotype Data for Eastern Massasauga Rattlesnakes (Sistrurus catenatus) from Bois Blanc Island, Michigan at 15 Microsatellite DNA Loci We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. These data are from 102 individual Eastern Massasauga Rattlesnakes sampled at Bois Blanc Island, Michigan and genotyped at 15 microsatellite loci. Samples were collected as part of a study to examine functional connectivity for the Eastern Massasauga. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration... Categories: Data; Tags: Bois Blanc island, Ecology, Lake Huron, Land Use Change, Michigan, All tags... USGS Science Data Catalog (SDC), Wildlife Biology, biological population management, biota, endangered species, environment, evolution, genetic diversity, genetics, genotype, loci, microsatellite, Fewer tags Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA Dataset containing information for white-tailed deer samples from Ohio, Pennsylvania, Maryland, Virginia and New York, genotyped for 11 microsatellites markers. Marker OvirQ should not be used as it presents alleles inconsistent with reported pattern, with some alleles separated by only 1 base pair and inconsistent between runs. Projected coordinates representing sampling location are in a user-defined CRS, similar to USA Contiguous Albers Equal Area Conic: "+proj=aea +lat_1=29.3 +lat_2=45.3 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs". Categories: Data; Tags: Maryland, New York, Ohio, Pennsylvania, USGS Science Data Catalog (SDC), All tags... United States, Virginia, Wildlife Biology, Wildlife Disease, biota, genetics, population and community ecology, wildlife population management, Fewer tags Discovery of Two Biological Mechanisms for Acetylene Metabolism in a Single Organism Acetylene fermentation assays, nitrogen fixation assays, and growth studies were performed with Pelobacter sp. strain SFB93 and Pelobacter acetylenicus DSM3246. Data includes concentrations of acetylene and ethylene over time, and growth measured with OD680 and cell counts. Categories: Data; Types: Citation; Tags: Ecology, Environmental Health, Genetics, Geochemistry, NA, All tags... USGS Science Data Catalog (SDC), Water Quality, Water Resources, acetylene, bacteria, nitrogen, Fewer tags Data relating to the development of a quantitative PCR assay for detecting Northwest salamander (Ambystoma gracile) in environmental DNA samples 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, All tags... biota, environmental DNA, Fewer tags Microsatellite data, boundaries of subpopulation centers, and estimated effective migration for greater sage-grouse collected in western North America between 1992 and 2015 (ver. 2.0, December 2022) Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Here, we characterized population structure and estimated effective migration in Greater Sage-grouse (Centrocercus urophasianus). Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation... Categories: Data, Data Release - Revised; Tags: Genetics, Subpopulation Center, USGS Science Data Catalog (SDC), Western North America, biota Rusty Patched Bumble Bee Pollen Metagenome The rusty-patched bumble bee (Bombus affinis) is a listed species under the Endangered Species Act of the United States. While understood to be a highly generalist forager, little is known on the role that limited floral resources or shifting floral community composition could have played in B. affinis decline. Determining which floral species provide suitable B. affinis forage could assist conservation efforts where B. affinis persists, identify floral species for restoration efforts, or highlight regions to search for cryptic populations. Categories: Data; Tags: Bombus affinis, Ecology, Environmental Health, Genetics, ITS2 Metagenome, All tags... Massachusetts, Michigan, Minnesota, New Jersey, New York, Pennsylvania, USGS Science Data Catalog (SDC), Wildlife Biology, Wisconsin, biota, bumblebee, museum specimen, pollen, Fewer tags Environmental DNA metabarcoding as a tool for biodiversity assessment and monitoring: Reconstructing established fish communities of north-temperate lakes and rivers To evaluate the ability of precipitation-based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well-studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on traditional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predicts eDNA detection. Fish community composition was estimated for seven lakes and two MIssissippi River navigation pools using sequence data from the mitochonrial 12S gene amplified from 10 to... Categories: Data; Tags: 12S gene, Aquatic Biology, Crystal Lake, Genetics, Lake Mendota, All tags... Lake Wingra, McDermott Lake, Sparkling Lake, Trout Bog, Trout Lake, USGS Science Data Catalog (SDC), Wisconsin lakes, biota, community ecology, environmental DNA, environmental DNA, fisheries, habitat, metagenomics, none, upper Mississippi River, upper Mississippi River Pool 13, upper Mississippi River Pool 19, Fewer tags Cyanotoxin, chlorophyll-a, and cyanobacterial toxin genetic data for samples collected at eleven large river sites throughout the United States, June through October 2018 This U.S. Geological Survey (USGS) data release provides discretely measured cyanotoxin, chlorophyll-a, and cyanobacterial toxin genetic data for samples collected from eleven large river sites throughout the United States, from June through October 2018. Discrete water-quality samples were analyzed for cyanotoxins (anatoxin, cylindrospermopsin, microcystin, and saxitoxin), chlorophyll-a, and cyanobacterial toxin genetics as part of a National Water-Quality Assessment Project pilot study to describe cyanobacteria and cyanotoxin occurrence in the Nation's large rivers. Categories: Data; Tags: Anatoxin, Aquatic Biology, California, Chattahoochee River near Whitesburg, GA, Chlorophyll-a, All tags... Connecticut, Connecticut River at Thompsonville, CT, Contaminants, HABS, Cyanotoxin genetics, Cyanotoxins, Cylindrospermopsin, Delaware River at Trenton, NJ, Discretely measured, Dolichospermum (formerly Anabaena), Ecology, Environmental Health, Enzyme-linked immunosorbent assay (ELISA), Genetics, Georgia, Kansas, Kansas River at De Soto, KS, Limnology, Maryland, Microcystin, Microcystis, Minnesota, Mississippi River at Hastings, MN, Missouri, Missouri River at Hermann, MO, New Jersey, Ohio, Ohio River at Cannelton Dam at Cannelton, IN, Oregon, Pheophytin-a, Phytoplankton community composition, Planktothrix, Quantitative polymerase chain reaction (qPCR), Sacramento River at Freeport, CA, Saxitoxin, Susquehanna River at Conowingo, MD, Texas, Trinity River below Dallas, TX, USGS Science Data Catalog (SDC), USGS Station ID 01184000, USGS Station ID 01463500, USGS Station ID 01578310, USGS Station ID 02338000, USGS Station ID 03303280, USGS Station ID 05331580, USGS Station ID 06892350, USGS Station ID 06934500, USGS Station ID 08057410, USGS Station ID 11447650, USGS Station ID 14211720, United States, Water, Water Quality, Water Quality, Water quality, Willamette River at Portland, OR, anaC gene, cyrA gene, mcyE gene, sxtA gene, Fewer tags Fish community assessment using environmental DNA metabarcoding data after an invasive species eradication and native restocking effort in Pinecrest Gardens, FL in 2017-18 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), All tags... Wildlife Biology, Wildlife Biology, biological population management, boundaries, environmental DNA, fish, genetic diversity, invasive species, Fewer tags Data from Burmese pythons swabbed for the presence of SFD-causing Ophidiomyces in southwest Florida The size and sex of each of the Burmese pythons swabbed in this study for the SFD-causing (snake fungal disease) Ophidiomyces ophiodiicola pathogen is given along with the real time PCR swab result. Categories: Data; Tags: Ecology, Florida, Genetics, Southern Florida, USGS Science Data Catalog (SDC), All tags... Wildlife Disease, biota, disease vectors, environment, invasive species, reptiles, wildlife disease, Fewer tags Novel genetic resources to facilitate future molecular studies in freshwater mussels (Bivalvia: Unionidae) Here we provide public access to six DNA sequence alignments and details on all specimens utilized in Smith and Johnson (2020). Categories: Data; Tags: DNA, USGS Science Data Catalog (SDC), biota, conservation, freshwater mussel, All tags... genetics, Fewer tags Molecular resources for investigating relationships among freshwater mussels (Bivalvia: Unionoida) with a focus on the genus Alasmidonta Longstanding taxonomic uncertainties have limited conservation efforts for species currently assigned to the freshwater mussel genus Alasmidonta. Here, we present mitochondrial and nuclear DNA sequence data needed to assess the genus- and species-level taxonomy of Alasmidonta. These molecular data allowed us to test whether cryptic diversity exists within Alasmidonta and whether A. triangulata and A. arcula are distinct species. Details associated with specimens and DNA sequence data are provided here to provide a foundation for future research on Alasmidonta and give conservation agencies greater confidence in the findings of our work. Categories: Data; Tags: DNA sequencing, Genetics, USGS Science Data Catalog (SDC), biota, conservation genetics, All tags... cryptic species, endangered species, generic reclassification, incomplete lineage sorting, integrative taxonomy, phylogenetic systematics, species delimitation, species diversity, systematics and taxonomy, Fewer tags Single Nucleotide Polymorphism (SNP) genomic data of moose (Alces alces) from the contiguous United States, 2009-2017 We analyzed the single nucleotide polymorphisms (SNPs) present in the genomes of moose representing 3 subspecies in the contiguous United States. Blood samples were collected opportunistically from collaborators during field efforts or were supplied to our lab from collaborators' archives, and represented moose sampling occurring between 2009-2017. DNA was extracted, sequenced using next generation sequencing, and SNPs analyzed using the genetics programs Structure and Tess3, and by performing basic population statistics. These analyses were used to determine the population structure of moose at the subspecies level. Categories: Data; Tags: Aquatic Biology, DNA sequencing, Ecology, Ecology, Genetics, All tags... Genetics, Idaho, Minnesota, Montana, New Hampshire, USGS Science Data Catalog (SDC), United States, Wildlife Biology, Wildlife Biology, Wyoming, genetics, mammals, Fewer tags Enteroctopus Sampling Effects on Genetic Data, Prince William Sound, Alaska, 2012-2015 These are genetic data collected from replicated samples of 21 Enteroctopus (E. dofleini or a cryptic lineage) in Prince William Sound Alaska to evaluate tissue type, DNA extraction method, and time until analyses are completed on data reliability. Data collected from all samples include two microsatellites identified as possible lineage indicators, and nine microsatellite loci previously identified as polymorphic in both lineages. DNA sequence data from 528 bp of the octopine dehydrogenase (OCDE) gene were also collected. Categories: Data; Tags: Amino Acid Oxidoreductases, Animals/Invertebrates, Bald Head Chris Island, Biodiversity, Biodiversity, All tags... Biota, Cephalopods, Chenega, DNA, DNA sequencing, Electrophoresis, Environment, Genetic Markers, Genetic diversity, Genetics, Golden Bay, Port Wells, Herring Bay, Long Bay, Marine ecosystems, Microsatellite Repeats, Mollusks, Polymerase chain reaction, Population genetics, Port Wells, Prince William Sound, Prince of Wales Passage, Species diversity, Systematics and taxonomy, USGS:ASC145, Western Prince William Sound, Fewer tags Spatial and temporal surveys of salmon eDNA in Seattle urban creeks, Washington, 2018 - 2020 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. Categories: Data; Tags: Aquatic Biology, Ecology, Genetics, Lake Washington, Seattle, All tags... USGS Science Data Catalog (SDC), environment, environmental DNA, fish, migratory species, salmon, urban streams, Fewer tags 1 2 3 4 5 ... 7 »