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.

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.

OTU sequence reads by sample, along with assigned taxonomy. This dataset is associated with the following publication: Bagley, M., E. Pilgrim, M. Knapp, C. Yoder, J. Santodomingo, and A. Banerji. High-throughput environmental DNA analysis informs a biological assessment of an urban stream. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 104: 378-389, (2019).

OTU sequence reads by sample, along with assigned taxonomy. This dataset is associated with the following publication: Bagley, M., E. Pilgrim, M. Knapp, C. Yoder, J. Santodomingo, and A. Banerji. High-throughput environmental DNA analysis informs a biological assessment of an urban stream. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 104: 378-389, (2019).

Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of fish and marine mammal species whose DNA has been detected in water samples collected between 2019 and 2021 using the mitochondrial marker MiFish (12S). The surveys were carried out in the summer of 2019 (July 14-18) and (July 30 - August 5), in the fall of 2020 (October 27-28) and in the summer-fall of 2021 (May 31 - June 3 ) and (August 24-25) between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 1-50 meters depth in 91 stations, with 1 to 3 replicates per station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissues or PowerWater extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. The libraries were prepared either by Génome Québec (2019, 2020) or by the Genomics Laboratory of the Maurice-Lamontagne Institute (2021), then sequenced on a NovaSeq 4000 PE250 system by Génome Québec. The bioinformatics analysis of the sequences obtained was carried out using an analysis pipeline developed in the genomics laboratory. A first step made it possible to obtain a table of molecular operational taxonomic units (MOTU) using the cutadapt software for the removal of the adapters and the R package DADA2 for the filtration, the fusion, removal of chimeras and compilation of data. The MOTUs table was then corrected using the R package metabaR to eliminate the tag-jumping and take contaminants into consideration. Samples showing a strong presence of contaminating MOTUs were removed from the dataset. The MOTUs were also filtered to remove all remaining adapter sequences and also retain only those of the expected size (around 170 bp). Finally, taxonomic assignments were made on the MOTUs using the BLAST+ program and the NCBI-nt database. Taxonomic levels (species, genus or family) were assigned using a best match method (Top hit), with a threshold of 95%. Only assignments at the level of fish and marine mammals were considered, and the taxa detected were compared to a list of regional species, and corrected if necessary. The species detections of the different replicas have been combined. The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute. This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems. Data were also published on SLGO platform : https://doi.org/10.26071/ogsl-2239bca5-c24a

These environmental DNA data and corresponding water quality data were collected and analyzed by the Fish and Wildlife Service in 2017. The samples were collected from 4 sites in pools 17 and 18 in the Upper Mississippi River on 3 sampling trips. The data was used to study occupancy modeling of eDNA data and determine optimal sampling effort required for reliable detection of invasive Bighead Carp and Silver Carp in streams with similar attributes at the Mississippi River.

The data sets contains hierarchical taxonomic identification information for DNA sequences detected in water samples from 5 locations.

A survey of environmental DNA was performed in Tunison Creek downstream of the USGS Tunison Aquatic Laboratory. The goal of the survey was to characterize the source ecological community at multiple trophic or taxonomic levels by associating DNA fragments with reference databases. Three taxonomically informative genetic loci were used: the mitochondrial cytochrome oxidase 1 locus, the mitochondrial 12S ribosomal locus, and the bacterial/organellar 16S ribosomal locus. The data set includes a list of sample and sequence accessions residing in the National Center for Biotechnology Information databases, which provide the raw data for analysis or re-use. The data also includes the representative sequences of operational taxonomic units (OTUs) and their abundance and taxonomic assignment, which are the primary endpoints of the data collection.

Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of invertebrates species whose DNA has been detected in water samples collected at 2018 using the marker COI. The surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 9-52 meters depth in 40 stations with one sample par station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissue extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. Libraries at the COI locus were prepared by Genome Quebec and sequenced on an Illumina MiSeq PE250 system. The bioinformatics analysis of the sequences obtained was carried out using an in-house analysis pipeline as reported in Bourret et al. 2022. A first step made it possible to obtain a molecular operational taxonomic unit table (MOTU) using the cutadapt software for the removal of the adapters and the DADA2 R package for the filtration, fusion, chimera removal and data compilation. The MOTUs table was subsequently corrected by taking into account the negative controls, where the number of observations in the latter was removed from the linked samples. Singleton MOTUs have also been removed. Finally, the taxonomic assignments were carried out on the MOTUs using the IDTAXA classifier (present in the DECIPHIER R package) using a training set trained on the COI reference bank for Golf St-Laurent (GSL-rl v1.0, https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) and a threshold of 40. Detections with an “Unreliable due to gaps” category were reported at the genus level only. The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute. This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems. Data are also available on SLGO platform : https://doi.org/10.26071/ogsl-cd4c205b-f63b

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).