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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.
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...
This dataset provides spatial predictions of habitat suitability for Gopherus agassizii (Agassiz’s desert tortoise), Gopherus morafkai (Morafka’s desert tortoise) and a pooled-species model under current conditions (1950 – 2000 yr). The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to evaluate subtle ecological niche differences between G. agassizii and G. morafkai, and identify local species-environment relationships. Spatial predictions of habitat suitability were created using MaxEnt version 3.4.0 (Phillips et al., 2006), a widely-used software for SDM in presence-background frameworks. Detailed methods are provided in Inman et al. 2019. Inman et al. 2019. Local niche...
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...
The fathead minnow (Pimephales promelas) is a key model of vertebrate toxicity. Standardized tests of toxicity in fathead minnow have been developed to support regulatory science, and much is known about the response of the species to various environmental pollutants. However, there is little data on genetic variation within the species, despite the potential influence of genetic background on toxicological outcomes. Furthermore, the phylogenetic relationships among Pimephales species are not fully established and rates of evolutionary divergence within the species and genus have not been investigated. This study examined patterns of genetic variation across the genome within a single wild population of fathead...
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 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.
Data describe a designed environmental DNA (eDNA) survey for the detection of longnose darter (Percina nasuta) in field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater fish 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 longnose darter DNA. Samples were collected from sites on the St. Francis river, Missouri in 2018.
Data consist of genotypes for pallid sturgeon and paddlefish broodstock and artificially-produced larvae at 19 sturgeon microsatellite loci and four paddlefish loci. Microsatellite genotypes allowed confirmation of homozygous sturgeon DNA and absence of paddlefish DNA in haploid gynogens. Data also consist of DNA yield estimates for haploid gynogens for proof of concept that haploid gynogens can provide sufficient DNA quantity for restriction site-associated DNA sequencing studies.
These data were compiled to provide seed transfer and native plant materials development guidance to managers and practitioners across the Colorado Plateau and in adjacent regions. This data release contains empirical seed transfer zones derived from molecular genetic data for Cleome lutea (syn. Peritoma lutea) and Machaeranthera canescens (syn. Dieteria canescens). These species show distinct population structure (i.e., genetic differentiation) across their ranges; as such, seed transfer zones reflect both patterns of genetic differentiation and information on each species' unique adaptations to climatic gradients. These shapefile data may support successful restoration outcomes if, for example, seed transfer follows...
The Aga, also known as the Mariana Crow, is an endangered endemic crow of the Northern Mariana Islands, a Commonwealth of the United States of America. The only known population currently extant is on the island of Rota and has been in decline over the past two decades. Unknown pathogens are among the factors that may be contributing to this decline. To support metagenomic and transcriptomic analysis of potential disease agents, a reference genome was generated and gene features comprehensively annotated. The methods used and data availability are described. This data release consists of: 1. Gene annotations for the endangered Aga or Mariana Crow, including summary statistics, that are available from the National...
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
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,
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,
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...
Monitoring the community structure and metabolic activities of cyanobacterial blooms in Upper Klamath Lake, Oregon, is critical to lake management because these blooms degrade water quality and produce toxic microcystins that are harmful to humans, domestic animals, and wildlife. Genetic tools, such as DNA fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analysis, high-throughput DNA sequencing (HTS), and real-time, quantitative polymerase chain reaction (qPCR) provide more sensitive and rapid assessments of bloom ecology than traditional techniques. The objectives of this study were (1) to characterize the microbial community at one site in Upper Klamath Lake and determine changes in...
Categories: Data;
Types: Citation;
Tags: Genetics,
USGS Science Data Catalog (SDC),
Upper Klamath Lake,
population dynamics, algal blooms, ecology, water quality
These data represent the standard curve values as well as measurements of cytokine and reference gene transcripts from blood samples collected from Florida manatees and quantified using quantitative PCR.
Categories: Data;
Tags: Aquatic Biology,
Crystal River,
Genetics,
Titusville,
USGS Science Data Catalog (SDC),
The 53 papers in this proceedings include a section celebrating the 25-year anniversary of the Shrub Sciences Laboratory (4 papers), three sections devoted to themes, genetics, and biodiversity (12 papers), disturbance ecology and biodiversity (14 papers), ecophysiology (13 papers), community ecology (9 papers), and field trip section (1 paper). The anniversary session papers emphasized the productivity and history of the Shrub Sciences Laboratory, 100 years of genetics, plant materials development for wildland shrub ecosystems, and current challenges in management and research in wildland shrub ecosystems. The papers in each of the thematic science sessions were centered on wildland shrub ecosystems. The field...
Categories: Publication;
Types: Citation;
Tags: biodiversity,
community ecology,
disturbance,
ecophysiology,
genetics,
This dataset provides spatial predictions of clustering and the genotype association index for the Mojave genotype in local species-environment relationships of Desert Tortoises (Gopherus agassizi and Gopherus morafkaii) for individuals in the subregion encompassing the genetic sampling locations used by Edwards et al. (2015). This region offered an opportunity to explore habitat selection across the ecotone between the Mojave and Sonoran deserts and the secondary contact zone between G. agassizii and G. morafkai, and is referred to as the focal study area. The raster layers contained here accompany the manuscript Inman et al. 2019 and were used to identify multivariate clusters and map them back to geographic space....
To understand the genetic structure of six rare plant species (Acanthomintha ilicifolia, Baccharis vanessae, Chloropyron maritimum ssp. maritimus, Deinandra conjugens, Dicranostegia orcuttiana, Monardella viminea), we obtained samples from known occurrences in San Diego County, prepared and sequenced ddRAD genomic libraries, and developed and analyzed a panel of genetic markers to assess population diversity and divergence. We provide this SNP genotype dataset in Structure format, produced in Stacks v2.0b8, for future monitoring efforts and population genetic analysis. These data support the following publication: Milano, E.R., and Vandergast, A.G., 2018, Population genomic surveys for six rare plant species in...
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