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.

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).

raw data for qPCR assays

This dataset is the evaluation of eutrophication in rivers based on quantitative polymerase chain reactions (qPCRs) of phytoplankton. The qPCR data of 2017, 2018, and 2019 are included in the current dataset. The 2917, 2018, and 2019 physicochemical and biological data generated by the USGS are also included in the current file. This dataset is associated with the following publication: Zhang, C., K. McIntosh, N. Sienkiewicz, E.A. Stelzer, J.L. Graham, and J. Lu. qPCR-based phytoplankton abundance and chlorophyll a: A multi-year study in twelve large freshwater rivers across the United States. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 954: 175067, (2024).

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.

These data are from EPA's national coastal monitoring programs and include data from the water column, sediments, and biota, 1990-2015. This dataset is associated with the following publication: Hale, S., H. Buffum, J. Kiddon, and M. Hughes. Subtidal Benthic Invertebrates Shifting Northward Along the U.S. Atlantic Coast. Estuaries and Coasts. Estuarine Research Federation, Port Republic, MD, USA, 40(6): 1744-1756, (2017).

These data are from EPA's national coastal monitoring programs and include data from the water column, sediments, and biota, 1990-2015. This dataset is associated with the following publication: Hale, S., H. Buffum, J. Kiddon, and M. Hughes. Subtidal Benthic Invertebrates Shifting Northward Along the U.S. Atlantic Coast. Estuaries and Coasts. Estuarine Research Federation, Port Republic, MD, USA, 40(6): 1744-1756, (2017).

This publication arises from a collaboration among federal agencies. U.S. EPA lead the water quality data collection, which is the data provided here. The data were obtained from ship-board sampling in spring and summer of 2017. This dataset is associated with the following publication: Kirkendall, D., D. Bunnell, P. Armenio, L. Eaton, A. Trebitz, and N. Watson. Spatial and temporal distributions of Dreissena spp. veligers in Lake Huron: Does calcium limit settling success?. JOURNAL OF GREAT LAKES RESEARCH. International Association for Great Lakes Research, Ann Arbor, MI, USA, 47(4): 1040-1049, (2021).