This dataset contains quantitative results from, and covariate attributes of, environmental DNA water samples collected across multiple rivers in 2023. Samples were analyzed for eDNA of round goby in the Hudson River (NY), westslope cutthroat trout (Oncorhynchus clarkii lewisi) in Cherry Creek (MT), lake trout (Salvelinus namaycush) and Spectaclecase mussels (Cumberlandia monodonta) in Big Piney River (MO), and rainbow trout (O. mykiss) and Western Pearlshell (Margaritifera falcata) in Loggers Creek (ID).

Environmental DNA quantitative results at the PCR technical replicate level for the target species Arctic Grayling and covariate information associated with these eDNA samples.

The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska, and analyzed with quantitative PCR.The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska, and analyzed with quantitative PCR.

The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska, and analyzed with quantitative PCR.The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska, and analyzed with quantitative PCR.

The dataset is composed of four tables containing data collected during screening surveys for invasive Round Goby (Neogobius melanostomus) at 12 sites on the Eastern Erie Canal in New York between Oneida Lake and the Hudson River from 2016 to 2023. The sampling techniques and frequency of sampling were adapted over time to optimize the efficiency of the study effort. From 2016-2019 eDNA water sampling and traditional fish surveys using seining, trapping, and benthic trawling were conducted twice annually (spring and summer) at the 12 sites. From 2020-2022, eDNA water sampling and traditional fish surveys using benthic trawling and electrofishing were conducted twice annually (spring and summer). In 2023, benthic trawling and electrofishing were conducted once (summer). The 12 study sites were selected to be approximately equidistant apart (~ 20 km) while also taking advantage of suitable access points. Within a study site, the exact areas that were sampled were often staggered by 500 m or occasionally more in order to find appropriate habitat for each gear type (i.e., wadable habitat for seining and habitat free of snags for trawling). The first table "eDNAData" contains environmental DNA data, the second table "FishCaptureData" contains fish community data from the traditional fish sampling methods, the third table "GobyLWData" contains length and weight measurements for all captured Round Goby beginning in 2020, and the fourth table "SiteData" contains information on the 12 study sites.

The dataset is composed of four tables containing data collected during screening surveys for invasive Round Goby (Neogobius melanostomus) at 12 sites on the Eastern Erie Canal in New York between Oneida Lake and the Hudson River from 2016 to 2023. The sampling techniques and frequency of sampling were adapted over time to optimize the efficiency of the study effort. From 2016-2019 eDNA water sampling and traditional fish surveys using seining, trapping, and benthic trawling were conducted twice annually (spring and summer) at the 12 sites. From 2020-2022, eDNA water sampling and traditional fish surveys using benthic trawling and electrofishing were conducted twice annually (spring and summer). In 2023, benthic trawling and electrofishing were conducted once (summer). The 12 study sites were selected to be approximately equidistant apart (~ 20 km) while also taking advantage of suitable access points. Within a study site, the exact areas that were sampled were often staggered by 500 m or occasionally more in order to find appropriate habitat for each gear type (i.e., wadable habitat for seining and habitat free of snags for trawling). The first table "eDNAData" contains environmental DNA data, the second table "FishCaptureData" contains fish community data from the traditional fish sampling methods, the third table "GobyLWData" contains length and weight measurements for all captured Round Goby beginning in 2020, and the fourth table "SiteData" contains information on the 12 study sites.

qPCR detection results for Pacific Lamprey eDNA surveys from Western Washington Rivers and Streams. Water samples were collected via filtration and shipped to the laboratory for analysis. DNA was extracted from filters using commercially available extraction kits. Lab staff used two existing Pacific Lamprey qPCR eDNA surveys to screen DNA extracts for the presence of Pacific Lamprey DNA. Eight molecular replicates were run for each samples. Results presented in this table show the number of positive detections out of 8 for each sample and the corresponding mean Cq values for each sample with a detection.

qPCR detection results for Pacific Lamprey eDNA surveys from Western Washington Rivers and Streams. Water samples were collected via filtration and shipped to the laboratory for analysis. DNA was extracted from filters using commercially available extraction kits. Lab staff used two existing Pacific Lamprey qPCR eDNA surveys to screen DNA extracts for the presence of Pacific Lamprey DNA. Eight molecular replicates were run for each samples. Results presented in this table show the number of positive detections out of 8 for each sample and the corresponding mean Cq values for each sample with a detection.

Environmental DNA (eDNA) surveys have become important tools for monitoring aquatic biodiversity. Barcode sequencing of eDNA generates community profiles that, while potentially biased in both capture and amplification, can nonetheless yield high information content per unit cost. While factors affecting eDNA capture and amplification have been heavily studied, watershed-scale assessments of fish communities and our confidence in such have been less frequent. We performed an initial watershed-scale characterization of fish eDNA using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our bioinformatic approach included 1) direct estimation of sequencing error from unambiguous mappings (alignments) and simulation of error in taxonomic assignment under various mapping criteria; 2) binning of species based on inferred assignment error rather than by taxonomic rank; and 3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented for the St. Regis River, New York, United States, which supports a valuable recreational fishery and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. We found that 300 mL drawn through 25-mm filters yielded greater than 5 ng/µL DNA at most sites in August and September, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state-level checklist into 85 single-species bins and seven multispecies bins. Of 48 taxonomic bins actually observed in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants post-collection. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence.

Environmental DNA (eDNA) surveys have become important tools for monitoring aquatic biodiversity. Barcode sequencing of eDNA generates community profiles that, while potentially biased in both capture and amplification, can nonetheless yield high information content per unit cost. While factors affecting eDNA capture and amplification have been heavily studied, watershed-scale assessments of fish communities and our confidence in such have been less frequent. We performed an initial watershed-scale characterization of fish eDNA using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our bioinformatic approach included 1) direct estimation of sequencing error from unambiguous mappings (alignments) and simulation of error in taxonomic assignment under various mapping criteria; 2) binning of species based on inferred assignment error rather than by taxonomic rank; and 3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented for the St. Regis River, New York, United States, which supports a valuable recreational fishery and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. We found that 300 mL drawn through 25-mm filters yielded greater than 5 ng/µL DNA at most sites in August and September, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state-level checklist into 85 single-species bins and seven multispecies bins. Of 48 taxonomic bins actually observed in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants post-collection. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence.