We collected environmental DNA (eDNA) data from the Elwha River, home to the world’s largest dam removal project, to track the spatial and temporal patterns of species responses following dam removal. In total, we collected data for 11 different fish taxa, sampled at 25 sites ranging across 56 river kilometers in a wilderness river for 4 years following dam removal. We show that eDNA can effectively be used to determine whether fish have recolonized past former dams, and in some cases determine the spatial extent of that recolonization.

We collected environmental DNA (eDNA) data from the Elwha River, home to the world’s largest dam removal project, to track the spatial and temporal patterns of species responses following dam removal. In total, we collected data for 11 different fish taxa, sampled at 25 sites ranging across 56 river kilometers in a wilderness river for 4 years following dam removal. We show that eDNA can effectively be used to determine whether fish have recolonized past former dams, and in some cases determine the spatial extent of that recolonization.

A web-browser enabled (HTML) document and Excel file (Water quality parameters and DNA Sequence Reads) that contain detailed data used to inform results presented in publication. This dataset is associated with the following publication: Reschke, E., R. Ennis, and L. Harwell. Using eDNA as a viable fish monitoring approach in Northern Gulf estuarine habitats. ENVIRONMENTAL MONITORING AND ASSESSMENT. Springer, New York, NY, USA, 197: 1145, (2025).

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.

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.

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.

Removal of two dams on the Elwha River, Washington will help restore natural sediment processes to the coastal environment near the river mouth. We are interested in the responses of fish associated with shallow subtidal and intertidal habitats because they function as spawning and rearing habitat for many fish species including the ecologically important forage fish and federally protected species of Pacific salmon. Since 2006, we have been collecting species composition and size distribution of the intertidal/subtidal fish community in the Eastern and Central Strait of Juan de Fuca. Potential reference site and treatment sites (where sediment changes are expected to occur) were sampled on a monthly basis from April to September using a beach seine. We found over 45 species of fish, mostly juvenile stages, using this portion of the Strait of Juan de Fuca representing two groups- fish occurring in the water column and those living on or near the bottom. The water column species tended to be very abundant and included both migrants (e.g., juvenile salmon) and residents (surf smelt). Although the same species tended to be present each year, they often exhibited dramatic between year variability in abundance. This suggests the importance of using multiple years of data to evaluate changes resulting from dam removal. Treatment and reference areas exhibited some significant differences and we found seasonality in the fish assemblage structure. Our results suggest that some promising bio-indicators of short and long term change in sediment processes are: 1) numbers of species, 2) species diversity, 3) composition and sizes of benthic species, 4) abundance by life history stage of surf smelt, and 5) presence of migratory species like juvenile salmon. We will continue this work following dam removal to track the changes due to dam removal. For this project, the data was stored in .xls and access files.

This dataset provides USFS watershed improvement activities to barriers to upstream migration. This includes improving existing passage structures or removing them entirely. Structures include culverts, dams, diversion dams. Also included are where structures have been added to purposely create barriers to protect native populations from invasive species. Data include the planned fiscal year and planned cost, the completed fiscal year, approximate completed cost, and partners involved. Each AOP activity is displayed as a single point.,

The dataset is composed of six tables containing environmental DNA (eDNA) and electrofishing data from American eel (Anguilla rostrata) surveys conducted on parts of the Mohawk River watershed and tributaries to the Hudson River in New York. The dataset includes (a) eDNA data from 36 sites in the Mohawk River watershed and adjacent areas including parts of the Eastern Erie Canal, Mohawk River, and tributaries that were sampled in spring 2021 and again in summer 2021,(b) paired eDNA/electrofishing data from 15 sites on tributaries to the Hudson River that were sampled between 2020 and 2021, and (c) model output of predicted American eel density from all sites in the Mohawk River watershed and adjacent areas where eDNA was detected. The table "MohawkHudsonEel_MohawkScreening_eDNAData" contains eDNA data from the 36 sites in the Mohawk River watershed, the table "MohawkHudsonEel_MohawkScreening_SiteData" contains supporting information on the 36 sites in the Mohawk River watershed, the table "MohawkHudsonEel_HudsonTribCalibration_LWData" contains the length and weight for all American eel captured during electrofishing surveys from the 15 sites on tributaries to the Hudson River, the table "MohawkHudsonEel_HudsonTribCalibration_eDNAData" contains eDNA data from the 15 sites on tributaries to the Hudson River, the table "MohawkHudsonEel_HudsonTribCalibration_SiteData" contains supporting information on the 15 sites on tributaries to the Hudson River including the dimensions of the reaches where electrofishing was conducted, and the table "MohawkHudsonEel_MohawkScreening_DensityEstimate" contains predicted density of American eel estimated from eDNA concentration using linear regression from all sites in the Mohawk River watershed and adjacent areas where eDNA was detected.