Data from: Enabling quantitative eDNA monitoring in lotic ecosystems by incorporating hydrological characteristics and allometric scaling

This dataset accompanies the study “Enabling quantitative eDNA monitoring in lotic ecosystems by incorporating hydrological characteristics and allometric scaling” and contains environmental DNA (eDNA) quantification data from controlled mesocosm experiments and field surveys in lotic ecosystems in Flanders, Belgium. Data were collected between January–June 2023 and September 2023 and include droplet digital PCR (ddPCR)–based species-specific eDNA concentrations, metabarcoding-derived estimates, electrofishing observations, and hydrological covariates. The dataset links fish abundance, biomass, and allometrically scaled biomass to eDNA signals while accounting for river discharge and habitat characteristics, enabling quantitative, fishery-independent biodiversity monitoring in flowing waters.

Dataset

Data_eDNAQuantification_Clean.csv, created on the 31st of July 2025. This is the cleaned, ready-to-use dataset containing both mesocosm and field experimental data, both eDNA detections, as well as electrofishing data. This dataset can be used with the provided script Script_eDNAQuantification_Clean.R. It has the following columns: 

• ID: an identification number for easy sorting of the data.
• Method: detections arrise from either the mesocosm experiment (Mesocosm) or from observational surveys via either eDNA-based methods, or electrofishing activities (Field).
• FilterNo: If applicable, the filter code was given for the eDNA samples.
• VolumeFilteredMl: The volume of water filtered to obtain the eDNA sample, given in ml.
• MesocosmNo: The number of the tank in which the fish were kept is included.
• Group: Two size classes were used during the mesocosm experiment, Small vs. Large. Data lines from the field surveys are appointed NA values in this column.
• Date: collection/sampling date.
• Location: Relevant only for the field surveys. Data lines from the mesocosm experiment are appointed NA values in this column. The column includes the name of the studied river, and more detailed information relating to the exact placement of the sample within the study location.
• Species: Latin name of the species studied.
• AbundanceNo: Number of fish used or counted.
• BiomassG: Total ammount of biomass, given in grams.
• AlloBiomass: Allometrically scaled biomass, following Yates et al., 2021. Also given in grams.
• ddPCR1: Number of eDNA copies detected with the droplet digital primer probe assays (or primer assay in case of Barbatula barbatula) during the first technical/laboratory replicate and standardized over the volume of water filtered. Calculations provided via the Quantasoft software.
• ddPCR2: Number of eDNA copies detected with the droplet digital primer probe assays (or primer assay in case of Barbatula barbatula) during the second technical/laboratory replicate and standardized over the volume of water filtered. Calculations provided via the Quantasoft software.
• ddPCR3: Number of eDNA copies detected with the droplet digital primer probe assays (or primer assay in case of Barbatula barbatula) during the third technical/laboratory replicate and standardized over the volume of water filtered. Calculations provided via the Quantasoft software.
• ddPCR: Averaged concentration of eDNA calculated as the mean of the previously provided technical replicate values.
• RiverDischargeRate: Relevant only for the field surveys. Data lines from the mesocosm experiment are appointed NA values in this column. Calculated following Van Driessche et al., 2022.
• ddPCRRiazSample: eDNA concentration of the amplified Riaz fragment.
• MBRiazTotalReads: Total number of reads generated during amplification of the Riaz fragment.
• MBSpeciesAbsReads: Number of reads of the studies species resulting from the Riaz metabarcoding analyses.
• PercentageRiaz: Relative read abundance of the species compared to the total amount of Riaz eDNA amplified, i.e. the species-specific fraction.
• SpConcViaRiaz: the species-specific eDNA concentration (resembling the ddPCR measurements above), but this time derived from the metabarcoding analyses.
• Latitude: coordinates for the sampling location, added for mapping purposes.
• Longitude: coordinates for the sampling location, added for mapping purposes.
• Ruggedness: Terrain Ruggedness Index, extracted from a Digital Elevation Model using QGIS software, as a proxy for habitat heterogeneity.

Script

Script_eDNAQuantification_Clean.R, created on the 31st of July 2025. This R script contains the statistical analyses applied to the dataset in support of Van Driessche et al. (2026).