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We designed two new samplers for monitoring airborne particulates, including fungal and fern spores and plant pollen, that rely on natural wind currents (Passive Environmental Sampler) or a battery operated fan (Active Environmental Sampler). Both samplers are modeled after commercial devices such as the Rotorod® and the Burkard samplers, but are more economical and require less maintenance than commercial devices. We conducted wind tunnel comparisons of our two new samplers to Rotorod® samplers using synthetic polyethylene spheres (12 - 160 µm in diameter) to compare numbers and size range of particulates that are captured by the samplers. This dataset contains raw numbers of polyethylene spheres that were captured...
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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...
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Rapid ʽŌhiʽa Death (ROD) currently threatens ōhiʽa lehua (Metrosideros polymorpha) on Hawaiʽi Island. First identified in Puna in 2014, the disease has now spread island wide. Besides direct sampling of trees, environmental sampling could serve as an easier and broader strategy to detect Ceratocystis spp., the fungi causing ROD. Environmental sampling could also help monitor the effect of felling ROD infected trees. We developed Passive and Active Environmental Samplers and deployed them at a property in Puna, where both C. lukuohia, and C. huliohia had been detected, and where the land owner practiced the management method of felling infected trees. We set up 2 Active Environmental Samplers (modified mosquito traps...
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Positive and negative dreissenid mussel DNA quantitiative PCR results from environmental DNA water samples collected in Montana, Wisconsin and Minnesota to assess if environmental DNA can extend the seasonal window for dreissenid mussel early detection.
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We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicability of the present assays surpass previous methods for detecting T. bryosalmonae DNA from fish tissue and water samples.
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Environmental DNA (eDNA) detection tools are becoming increasingly popular for documenting occurrence and distribution of native and invasive species. These tools can allow early detection of new diseases and invasive species and provide critical information for land management. We designed two new samplers for monitoring airborne particulates, including fungal and fern spores and plant pollen, that rely on natural wind currents (Passive Environmental Sampler) or a battery operated fan (Active Environmental Sampler). This dataset contains results of an experiment that was designed to determine probability of detecting known numbers of Ceratocystis lukuohia spores on individual slides in these samplers.
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Data included are from a series of field sample collections from Lakes Michigan and Huron, and laboratory mesocosms targeting the round goby fish (Neogobius melanostomus). The round goby is a benthic fish that has heavily invaded four of the five Laurentian Great Lakes. Because it inhabits a variety of substrates, including coastal breakwaters, traditional methods (e.g., trawling, trapping) are inadequate to quantify overall population size. Environmental DNA (eDNA) may be a viable option for improving detection and quantification of the species. Field data include number of round goby caught and associated ambient conditions of the aquatic matrix (temperature, pH, turbidity, conductivity, dissolved oxygen). Mesocosm...
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These data include metadata and associated data files associated with the manuscript, "Economical Environmental Sampler Designs for Detecting Airborne Spread of Fungi Responsible for Rapid ʽŌhiʽa Death." These data include a total of 8 datasets used for both controlled and field studies evaluating the use of Active (with battery operated fan) and Passive (dependent on wind) USGS Environmental Samplers on Hawaii Island between 2016-2018. Samplers were operated under controlled laboratory and field conditions with a commercial sampler (Rotorod® Model 20) to compare efficacy in capturing synthetic polyethylene spheres (12 - 160 µm in diameter) and also Xyleborus spp. boring dust (frass) known to contain the fungi responsible...
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We designed two new samplers for monitoring airborne particulates, including fungal and fern spores and plant pollen, that rely on natural wind currents (Passive Environmental Sampler) or a battery operated fan (Active Environmental Sampler). Both samplers are modeled after commercial devices such as the Rotorod® and the Burkard samplers, but are more economical and require less maintenance than commercial devices. We compared our two new samplers to Rotorod® samplers using Xyleborus spp. boring dust known to contain ROD causing pathogens. The comparison was done in a large outdoor field cage to determine relative effectiveness of the three samplers for capturing windblown boring dust. The dataset contains results...
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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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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...
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These data contain all the raw results needed to support the conclusions for the final product. These data are water sampling locations (latitude and longitude), date of water sampling, quantitative PCR values for each water sample, and stream flow at USGS stream gauging stations on sampling day.
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eDNA-based spatiotemporal distribution data (occupancy model format) for rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) within the Bruneau-Jarbidge Rivers Wilderness in southern Idaho and northern Nevada, USA. Data also include stream discharge and stream temperature data for each site. All data were collected between October 2015 and September 2016.
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Environmental DNA (eDNA) water samples were collected at 15 tree islands containing wading bird breeding colonies (order Pelecaniformes) and 15 empty control islands in the central Everglades of Florida in spring of 2017 (April through June) and analyzed for the presence of eDNA from invasive Burmese pythons (Python bivittatus). The Burmese python is now established as a breeding population throughout south Florida, USA. Pythons can consume large quantities of prey and may be a particular threat to wading bird breeding colonies in the Everglades. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis—a genetic tool which detects shed DNA in water...
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...
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We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicability of the present assays surpass previous methods for detecting T. bryosalmonae DNA from fish tissue and water samples.
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Quantitative PCR data from mesocosm experiments and field evaluations comparing coarse filter-large water volume environmental DNA samples vs. fine filter-small water volume environmental DNA samples for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. Mesocosm experiments took place at the US Fish & Wildlife Service's Creston Fish Hatchery in Montana, 2016. Field surveys took place in the Flathead River basin of Montana, 2016.
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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.
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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.


map background search result map search result map Asian carp eggs cannot be distinguished from other cyprinid species on the basis of morphology alone: Supporting Data Wabash River, Indiana bigheaded carps environmental DNAs: Data A Protocol for Collecting Environmental DNA Samples From Streams Conventional and quantitative PCR assays for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples Conventional PCR results for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples Round goby eDNA survey, evaluation, and laboratory data in Lakes Michigan and Huron 2016-2017 Distribution and seasonal differences in Pacific Lamprey and Lampetra spp eDNA across 18 Puget Sound watersheds, 2014 and 2015 Environmental DNA mapping of Zebra Mussel populations: Data Hawaii Island Environmental Sampler Comparison 2016-2018 Orchidlands Estates Ceratocystis DNA Detection 2016 Ceratocystis lukuohia spore dilution for probit analysis Ceratocystis DNA Detection in Frass During Caged Sampler Comparison Polyethylene Particle Detection (counts) during Environmental Sampler Comparison Environmental DNA results from dreissenid mussel early detection surveys in Montana, Minnesota, and Wisconsin 2017-2018 Burmese python environmental DNA data, and environmental covariates, collected from wading bird aggregations and control sites in the Greater Everglades Ecosystem, United States, in 2017 Environmental DNA results for large and small volume water samples in mesocosm experiments at Creston Fish Hatchery and field surveys in the Flathead River Basin, MT in 2016 Bullseye snakehead environmental DNA data, and associated attributes, collected from southeast Florida, from 2015-2018 Occupancy data for spatiotemporal distribution assessments of bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) in the Bruneau and Jarbidge River Basins, Idaho and Nevada, USA, in water year 2016 Ceratocystis DNA Detection in Frass During Caged Sampler Comparison A Protocol for Collecting Environmental DNA Samples From Streams Polyethylene Particle Detection (counts) during Environmental Sampler Comparison Orchidlands Estates Ceratocystis DNA Detection 2016 Ceratocystis lukuohia spore dilution for probit analysis Hawaii Island Environmental Sampler Comparison 2016-2018 Burmese python environmental DNA data, and environmental covariates, collected from wading bird aggregations and control sites in the Greater Everglades Ecosystem, United States, in 2017 Occupancy data for spatiotemporal distribution assessments of bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) in the Bruneau and Jarbidge River Basins, Idaho and Nevada, USA, in water year 2016 Asian carp eggs cannot be distinguished from other cyprinid species on the basis of morphology alone: Supporting Data Environmental DNA results for large and small volume water samples in mesocosm experiments at Creston Fish Hatchery and field surveys in the Flathead River Basin, MT in 2016 Bullseye snakehead environmental DNA data, and associated attributes, collected from southeast Florida, from 2015-2018 Distribution and seasonal differences in Pacific Lamprey and Lampetra spp eDNA across 18 Puget Sound watersheds, 2014 and 2015 Wabash River, Indiana bigheaded carps environmental DNAs: Data Round goby eDNA survey, evaluation, and laboratory data in Lakes Michigan and Huron 2016-2017 Environmental DNA mapping of Zebra Mussel populations: Data Environmental DNA results from dreissenid mussel early detection surveys in Montana, Minnesota, and Wisconsin 2017-2018 Conventional PCR results for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples Conventional and quantitative PCR assays for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples