Environmental DNA detection results from samples collected using autonomous water sampling robots and manual approaches. Samples were collected in the Upper Yellowstone River (Montana) and Upper Snake River (Idaho/Wyoming) in 2018 and 2019. Samples were tested for the DNA of the following species: the waterborne protozoa Naegleria spp., the fish pathogen Tetracapsuloides bryosalmonae, Scomber japonicas (mackerel fish), kokanee salmon (Oncorhynchus nerka) and dreissenid mussel (Dreissena spp.).

Data described herein was collected by USGS personnel and the project funded by USGS. Northern snakehead specimens were collected from the Potomac River and its tributaries by regional natural resource management agencies in the course of their field investigations working with this priority invasive aquatic species. Specimens were provided to USGS for the purpose of conducting health related assessments of northern snakehead in the region, with approximately 90 specimens evaluated grossly and histologically for the presence of lesions and abnormalities. Data presented here was collected seasonally (spring through fall) in 2006 and from 2015 to 2017. Data for each specimen includes date and location of collection, morphometrics, gender (if known), and gross abnormalities, and histological lesions observed. This body of data is stored in spreadsheet format.

Data described herein was collected by USGS personnel and the project funded by USGS. Northern snakehead specimens were collected from the Potomac River and its tributaries by regional natural resource management agencies in the course of their field investigations working with this priority invasive aquatic species. Specimens were provided to USGS for the purpose of conducting health related assessments of northern snakehead in the region, with approximately 90 specimens evaluated grossly and histologically for the presence of lesions and abnormalities. Data presented here was collected seasonally (spring through fall) in 2006 and from 2015 to 2017. Data for each specimen includes date and location of collection, morphometrics, gender (if known), and gross abnormalities, and histological lesions observed. This body of data is stored in spreadsheet format.

This dataset includes field hydrologic measurements and laboratory analyses of surface and pore waters, sediments, benthic plants/biofilms, and biota along the Middle Snake River upgradient of the Hells Canyon Complex. The study region for this work focuses on a section of the Snake River heavily utilized for agriculture, with complex systems of irrigation diversion and return drainage, spanning 164 km above the Hells Canyon Complex (Idaho, Oregon). The goal of this study was to identify potential loading sources of methylmercury from the upgradient Snake River into the reservoir complex, with a focus on the tributaries, irrigation return drains, and riparian zones adjacent to agricultural lands along the river. To this end, 16 locations along the Snake River between River Miles 448 and 346 were sampled over a four-day period, July 11 – 14, 2022. At each sampling site, pore water and sediment cores were collected in the shallow riparian zones along the edge of the river, surface waters were collected from cross-sections of the river, river flow and velocity were measured, submerged macrophytes and associated biofilm was collected, and biota (snails, amphipods, clams, periphyton, dragonfly larvae) were sampled from shallow riparian margins using a boat-mounted benthic suction dredge. Concurrently, water samples were collected from the six major tributaries that enter the Snake River in the study reach (Succor Creek, Owyhee River, Boise River, Malheur River, Payette River, Weiser River) and from six irrigation return drains that were actively discharging to the Snake River. Data from additional irrigation return drains to the study reach, sampled in June 2021 and May 2022, are also included. All water samples (surface and pore water) were processed and analyzed for filter-passing total mercury and methylmercury, dissolved organic carbon (DOC), dissolved organic matter (DOM) composition (UV-vis absorption and fluorescence), inorganic anions (chloride, nitrate, sulfate), and filter acidified metals (iron, manganese). In addition, the surface waters were analyzed for total suspended solids (TSS), particulate total and methylmercury, particulate organic carbon (POC) and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, and particulate metals (iron, manganese); and the pore waters were analyzed for inorganic sulfide (S(-II)). Sediment, submerged macrophytes and biofilms, and biota samples were dried, ground, and analyzed for total and methylmercury. Loss on ignition was also measured on the sediment samples. This data release includes eight metadata and data tables in machine readable format (*.csv). All data columns in tables 3-8 are defined in Table 2. Reference Table 2 for associated units, abbreviation definitions, laboratory information, and method citations. Table_1_Site_Descriptions.csv - site descriptions Table_2_Analysis_Descriptions.csv - data dictionary defining column headings in Tables 3-8 Table_3_Water_SW.csv - surface water chemistry data Table_4_Water_PW.csv - pore water chemistry data Table_5_Sediment.csv - sediment chemistry data Table_6_Macrophytes_and_Biofilms.csv - submerged macrophyte and biofilm data Table_7_Hydrology.csv - hydrologic data Table_8_Biota.csv - biota data

This dataset includes field hydrologic measurements and laboratory analyses of surface and pore waters, sediments, benthic plants/biofilms, and biota along the Middle Snake River upgradient of the Hells Canyon Complex. The study region for this work focuses on a section of the Snake River heavily utilized for agriculture, with complex systems of irrigation diversion and return drainage, spanning 164 km above the Hells Canyon Complex (Idaho, Oregon). The goal of this study was to identify potential loading sources of methylmercury from the upgradient Snake River into the reservoir complex, with a focus on the tributaries, irrigation return drains, and riparian zones adjacent to agricultural lands along the river. To this end, 16 locations along the Snake River between River Miles 448 and 346 were sampled over a four-day period, July 11 – 14, 2022. At each sampling site, pore water and sediment cores were collected in the shallow riparian zones along the edge of the river, surface waters were collected from cross-sections of the river, river flow and velocity were measured, submerged macrophytes and associated biofilm was collected, and biota (snails, amphipods, clams, periphyton, dragonfly larvae) were sampled from shallow riparian margins using a boat-mounted benthic suction dredge. Concurrently, water samples were collected from the six major tributaries that enter the Snake River in the study reach (Succor Creek, Owyhee River, Boise River, Malheur River, Payette River, Weiser River) and from six irrigation return drains that were actively discharging to the Snake River. Data from additional irrigation return drains to the study reach, sampled in June 2021 and May 2022, are also included. All water samples (surface and pore water) were processed and analyzed for filter-passing total mercury and methylmercury, dissolved organic carbon (DOC), dissolved organic matter (DOM) composition (UV-vis absorption and fluorescence), inorganic anions (chloride, nitrate, sulfate), and filter acidified metals (iron, manganese). In addition, the surface waters were analyzed for total suspended solids (TSS), particulate total and methylmercury, particulate organic carbon (POC) and stable isotopic composition, particulate nitrogen (PN) content and stable isotopic composition, and particulate metals (iron, manganese); and the pore waters were analyzed for inorganic sulfide (S(-II)). Sediment, submerged macrophytes and biofilms, and biota samples were dried, ground, and analyzed for total and methylmercury. Loss on ignition was also measured on the sediment samples. This data release includes eight metadata and data tables in machine readable format (*.csv). All data columns in tables 3-8 are defined in Table 2. Reference Table 2 for associated units, abbreviation definitions, laboratory information, and method citations. Table_1_Site_Descriptions.csv - site descriptions Table_2_Analysis_Descriptions.csv - data dictionary defining column headings in Tables 3-8 Table_3_Water_SW.csv - surface water chemistry data Table_4_Water_PW.csv - pore water chemistry data Table_5_Sediment.csv - sediment chemistry data Table_6_Macrophytes_and_Biofilms.csv - submerged macrophyte and biofilm data Table_7_Hydrology.csv - hydrologic data Table_8_Biota.csv - biota data

Biological indicator taxa have long been used for integrative assessments of water quality, particularly benthic invertebrate groups such as arthropods. While standardized protocols have been developed to calculate 'biological index' scores based on the abundances of these taxa, such systems are challenging to implement at large scales due to the sampling effort required, taxonomic expertise needed, and the need for repeated sampling to reliably discriminate sites. Many of the same taxa detected by traditional surveys can also be detected by genetic analysis of environmental DNA (eDNA), potentially allowing for an alternative formulation of biological indexes that might be faster and more economical to produce. The current data were produced to evaluate eDNA-derived biological indexes at sites within the Potomac River watershed of the eastern United States, specifically within units of the National Park Service for which previous biological assessment data were available. This data release consists of five files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sample-derived sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All accessions listed in the file can be searched to retrieve sample and sequence information at www.ncbi.nlm.nih.gov. 2. cox1.references.fasta, which contains reference sequences of the cytochrome c oxidase 1gene of arthropods (typically abbreviated cox1 or COI), identified from regional checklists. The file is a text file in FASTA format. 3. mt16S.references.fasta, which contains reference sequences of the mitochondrial 16S ribosomal RNA (mt16S) gene of arthropods identified from regional checklists. The file is a text file in FASTA format. 4. first.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the first stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated. 5. second.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the second stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated.

Biological indicator taxa have long been used for integrative assessments of water quality, particularly benthic invertebrate groups such as arthropods. While standardized protocols have been developed to calculate 'biological index' scores based on the abundances of these taxa, such systems are challenging to implement at large scales due to the sampling effort required, taxonomic expertise needed, and the need for repeated sampling to reliably discriminate sites. Many of the same taxa detected by traditional surveys can also be detected by genetic analysis of environmental DNA (eDNA), potentially allowing for an alternative formulation of biological indexes that might be faster and more economical to produce. The current data were produced to evaluate eDNA-derived biological indexes at sites within the Potomac River watershed of the eastern United States, specifically within units of the National Park Service for which previous biological assessment data were available. This data release consists of five files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sample-derived sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All accessions listed in the file can be searched to retrieve sample and sequence information at www.ncbi.nlm.nih.gov. 2. cox1.references.fasta, which contains reference sequences of the cytochrome c oxidase 1gene of arthropods (typically abbreviated cox1 or COI), identified from regional checklists. The file is a text file in FASTA format. 3. mt16S.references.fasta, which contains reference sequences of the mitochondrial 16S ribosomal RNA (mt16S) gene of arthropods identified from regional checklists. The file is a text file in FASTA format. 4. first.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the first stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated. 5. second.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the second stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated.

This dataset contains information on all snakehead fishes found in the United States. It is a subset of a larger database, the Nonindigenous Aquatic Species Database (NAS). This information resource is an established central repository for spatially referenced biogeographic accounts of introduced aquatic species. The NAS website provides scientific reports, online/real-time queries, spatial data sets, distribution maps, fact sheets, and general information.

Environmental DNA (eDNA) detection of invasive species can be used to delimit occupied ranges and estimate probabilities to inform management decisions. Environmental DNA is shed into the environment through skin cells and bodily fluids and can be detected in water samples collected from lakes, rivers, and swamps. In south Florida, invasive Burmese pythons occupy much of the Greater Everglades in mostly inaccessible habitat and are credited with causing severe declines of native species’ populations. Detection of Burmese pythons by traditional methods, such as trapping and visual searching, have been largely ineffective, making eDNA a superior method for differentiating invaded habitat. We adapted a quantitative PCR eDNA assay for droplet digital PCR, a state-of-the-art method that improves precision and accuracy. From August 2014 to October 2016, locations in and around Arthur R. Marshall Loxahatchee National Wildlife Refuge in southeast Florida were surveyed for Burmese python eDNA. The Refuge is maintained to provide water storage and is considered one of the last remnants of the northern Everglades wetlands. Positive eDNA detections were made at each of the five sampling events, assessing a total of 399 samples, with moderate occurrence (ψ=58-91%) and detection (p=40-70%) probabilities, potentially reduced by high PCR inhibition-levels. The high occurrence rates and geographic distribution of the positive samples within the Refuge suggests a steady release of python eDNA from a resident Burmese python population and reduces support for primarily transport of eDNA through boats or flowing water from the north. The first confirmed sighting of a Burmese python in the Refuge occurred in September 2016, after eDNA testing had indicated the presence of pythons. An established population is not expected this far north, however, the detections likely indicate northern range limit of a consistent population at Loxahatchee on the eastern side of the Florida peninsula. Our study demonstrates the benefit of eDNA for determining more accurate range limits and expansion information for Burmese pythons, as well as laying the foundation for the assessment of control efforts.

The datasets used in the creation of the predicted Habitat Suitability models includes the CWHR range maps of Californias regularly-occurring vertebrates which were digitized as GIS layers to support the predictions of the CWHR System software. These vector datasets of CWHR range maps are one component of California Wildlife Habitat Relationships (CWHR), a comprehensive information system and predictive model for Californias wildlife. The CWHR System was developed to support habitat conservation and management, land use planning, impact assessment, education, and research involving terrestrial vertebrates in California. CWHR contains information on life history, management status, geographic distribution, and habitat relationships for wildlife species known to occur regularly in California. Range maps represent the maximum, current geographic extent of each species within California. They were originally delineated at a scale of 1:5,000,000 by species-level experts and have gradually been revised at a scale of 1:1,000,000. For more information about CWHR, visit the CWHR webpage (https://www.wildlife.ca.gov/Data/CWHR). The webpage provides links to download CWHR data and user documents such as a look up table of available range maps including species code, species name, and range map revision history; a full set of CWHR GIS data; .pdf files of each range map or species life history accounts; and a User Guide.The models also used the CALFIRE-FRAP compiled "best available" land cover data known as Fveg. This compilation dataset was created as a single data layer, to support the various analyses required for the Forest and Rangeland Assessment, a legislatively mandated function. These data are being updated to support on-going analyses and to prepare for the next FRAP assessment in 2015. An accurate depiction of the spatial distribution of habitat types within California is required for a variety of legislatively-mandated government functions. The California Department of Forestry and Fire Protections CALFIRE Fire and Resource Assessment Program (FRAP), in cooperation with California Department of Fish and Wildlife VegCamp program and extensive use of USDA Forest Service Region 5 Remote Sensing Laboratory (RSL) data, has compiled the "best available" land cover data available for California into a single comprehensive statewide data set. The data span a period from approximately 1990 to 2014. Typically the most current, detailed and consistent data were collected for various regions of the state. Decision rules were developed that controlled which layers were given priority in areas of overlap. Cross-walks were used to compile the various sources into the common classification scheme, the California Wildlife Habitat Relationships (CWHR) system.CWHR range data was used together with the FVEG vegetation maps and CWHR habitat suitability ranks to create Predicted Habitat Suitability maps for species. The Predicted Habitat Suitability maps show the mean habitat suitability score for the species, as defined in CWHR. CWHR defines habitat suitability as NO SUITABILITY (0), LOW (0.33), MEDIUM (0.66), or HIGH (1) for reproduction, cover, and feeding for each species in each habitat stage (habitat type, size, and density combination). The mean is the average of the reproduction, cover, and feeding scores, and can be interpreted as LOW (less than 0.34), MEDIUM (0.34-0.66), and HIGH (greater than 0.66) suitability. Note that habitat suitability ranks were developed based on habitat patch sizes >40 acres in size, and are best interpreted for habitat patches >200 acres in size. The CWHR Predicted Habitat Suitability rasters are named according to the 4 digit alpha-numeric species CWHR ID code. The CWHR Species Lookup Table contains a record for each species including its CWHR ID, scientific name, common name, and range map revision history (available for download at https://www.wildlife.ca.gov/Data/CWHR).