DOI: 10.5061/dryad.r4xgxd2jh
title: Data for: Detection and quantification of two commercial flatfishes (Solea solea and Pleuronectes platessa) in the North Sea using environmental DNA

description: Sustainable fisheries management requires regular scientific monitoring of
 fish stocks. When information on certain fish stocks is limited,
 environmental DNA (eDNA) holds promise to complement traditional
 monitoring surveys. However, a better understanding of how eDNA
 concentrations relate to fish abundance and biomass is needed. Here, eDNA
 quantification of two commercially important flatfish species in the
 North‐East Atlantic, common sole (Solea solea) and European plaice
 (Pleuronectes platessa), was assessed. First, species‐specific,
 probe‐based assays for plaice and sole targeting the mitochondrial
 cytochrome b and cytochrome c oxidase subunit I gene, respectively, were
 developed (for sole) and validated (for both species). Subsequently, two
 mesocosm experiments revealed a significant and positive relationship
 between both abundance and biomass and eDNA concentrations for both
 species at three eDNA emission time periods (5 min, 1 h, and 24 h). Larger
 plaice shed significantly more eDNA (copies L-1) than smaller
 conspecifics. Finally, eDNA was obtained from seawater collected during
 research surveys in the Belgian part of the North Sea in spring 2020
 (i.e., local scale) and the southwestern North Sea in autumn 2020 and 2021
 (i.e., regional scale). eDNA concentrations were compared to the observed
 abundance (individuals per km2) and fish density in terms of biomass (kg
 per km2) as observed in the trawl at the same station. Local eDNA
 concentrations of both sole and plaice were positively correlated with
 observed abundance and fish density. The correlation between regional eDNA
 concentrations and fish density was positive and significant for sole in
 2020 and 2021 and for plaice in 2020, but not in 2021. The correlation
 between regional eDNA concentrations and observed abundance was positive
 and significant for sole and plaice in 2020, but not in 2021. These
 results illustrate the potential of eDNA to estimate abundance and biomass
 parameters for stock assessments of flatfishes in the North Sea.
description: See the Material and Methods section of the associated
 publication.
description: # Data for: Detection and quantification of two commercial flatfishes
 (Solea solea and Pleuronectes platessa) in the North Sea using
 environmental DNA Dataset DOI:
 [10.5061/dryad.r4xgxd2jh](https://doi.org/10.5061/dryad.r4xgxd2jh) ##
 Description of the data and file structure Environmental DNA (eDNA) offers
 a non-invasive method to monitor fish stocks, complementing traditional
 surveys. This study focuses on quantifying eDNA of two commercially
 important flatfish species, common sole (*Solea solea*) and European
 plaice (*Pleuronectes platessa*) in the North Sea. Species-specific assays
 were developed and validated. Mesocosm experiments revealed a strong
 correlation between eDNA concentration and fish abundance/biomass.
 Field-collected seawater samples from Belgian and southwestern North Sea
 surveys (2020–2021) showed significant correlations between eDNA and
 trawl-based observations, demonstrating the potential of eDNA for stock
 assessments. This dataset includes data from mesocosm experiments and
 field surveys in the North Sea, alongside specificity files for assay
 validation. See the Materials and Methods section of the associated
 publication for details on experimental design and data processing. ###
 Files and variables #### File: Mesocosm_plaice.csv **Description:** This
 dataset contains eDNA concentrations measured in controlled mesocosm
 experiments designed to assess eDNA shedding by plaice over time. The
 experiments evaluated the relationship between fish size, biomass, and
 eDNA concentrations at multiple time points. ##### Variables * Sample:
 Unique identifier for each sample, including tank and time point
 information. * Time: Time elapsed since start of the experiment (e.g., 0,
 5 min, 1 hour, 24 hours). * Tank: Identifier for the mesocosm tank where
 fish were held. * Concentration (cop/l): Raw eDNA concentration measured
 in copies per liter (copies/L). * LogConcentration (cop/l): Logarithm
 (base 10) of the eDNA concentration (copies/L), for normalization. *
 Size: Size category of fish in the tank (e.g., Small, Large). *
 Biomass: Total biomass (in grams) of fish present in the tank. #### File:
 Mesocosm_sole.csv **Description:** This dataset contains eDNA
 concentrations measured in controlled mesocosm experiments aimed at
 studying eDNA shedding dynamics of common sole over different time
 intervals. The data includes eDNA concentrations in relation to fish
 biomass held in each tank. ##### Variables * sample: Unique identifier for
 each sample, indicating tank and time point. * Time: Time elapsed since
 the start of the experiment (e.g., 5 min, 1 hour, 24 hours). *
 Tank: Identifier for the mesocosm tank where fish were kept. *
 TargetConcentrationSample(cop/l): Measured eDNA concentration in copies
 per liter (copies/L). * Biomass: Total biomass of fish present in the tank
 (grams). #### File: AMK2020.csv **Description:** This file contains
 environmental DNA (eDNA) and fisheries trawl data collected during the AMK
 2020 research campaign in the Belgian part of the North Sea. The dataset
 includes eDNA concentrations for common sole (*Solea solea*) and plaice
 (*Pleuronectes platessa*), as well as their corresponding trawl-based
 catch per unit effort (CPUE) and estimated abundance. ##### Variables *
 Campaign: Name of the sampling campaign (e.g., AMK2020). * Station: Unique
 identifier for each sampling location. * Sole_eDNA: Measured eDNA
 concentration for *Solea solea* (copies/L). * Plaice_eDNA: Measured eDNA
 concentration for *Pleuronectes platessa* (copies/L). *
 SoleCPUE_ob: Observed catch per unit effort for *Solea solea* (kg/km²)
 from trawl survey. * PlaiceCPUE_ob: Observed catch per unit effort for
 *Pleuronectes platessa* (kg/km²) from trawl survey. *
 Sole_eDNA_withoutlier: eDNA concentration for *Solea solea* with
 statistical outliers removed. * Plaice_eDNA_withoutlier: eDNA
 concentration for *Pleuronectes platessa* with statistical outliers
 removed. * Sole_abundance: Estimated abundance of *Solea solea*
 (individuals/km²). * Plaice_abundance: Estimated abundance of
 *Pleuronectes platessa* (individuals/km²). #### File: BTS2020.csv
 **Description:** This file contains eDNA and fisheries trawl data
 collected during the BTS 2020 research campaign in the southwestern North
 Sea. It includes eDNA concentrations for sole* *and plaice, alongside
 trawl-based catch per unit effort (CPUE) and abundance estimates. #####
 Variables * Campaign: Name of the sampling campaign (e.g., BTS2020). *
 Station: Unique identifier for each sampling location. *
 Sole_eDNA: Measured eDNA concentration for *Solea solea* (copies/L). *
 Plaice_eDNA: Measured eDNA concentration for *Pleuronectes platessa*
 (copies/L). * SoleCPUE_ob: Observed catch per unit effort for *Solea
 solea* (kg/km²) from trawl survey. * PlaiceCPUE_ob: Observed catch per
 unit effort for *Pleuronectes platessa* (kg/km²) from trawl survey. *
 Sole_eDNA_withoutlier: eDNA concentration for *Solea solea* with outliers
 removed (method 1). * Sole_eDNA_withoutlier1: eDNA concentration for
 *Solea solea* with outliers removed (method 2). *
 Sole_abundance: Estimated abundance of *Solea solea* (individuals/km²). *
 Plaice_abundance: Estimated abundance of *Pleuronectes platessa*
 (individuals/km²). #### File: BTS2021.csv **Description:** This file
 contains eDNA and fisheries trawl data collected during the BTS 2021
 research campaign in the southwestern North Sea. It includes eDNA
 concentrations and trawl survey data for sole and plaice. ##### Variables
 * Campaign: Name of the sampling campaign (e.g., BTS2021). *
 Station: Unique identifier for each sampling location. * Sole_eDNA:
 Measured eDNA concentration for *Solea solea* (copies/L). *
 Plaice_eDNA: Measured eDNA concentration for *Pleuronectes platessa*
 (copies/L). * SoleCPUE_ob: Observed catch per unit effort for *Solea
 solea* (kg/km²) from trawl survey. * PlaiceCPUE_ob: Observed catch per
 unit effort for *Pleuronectes platessa* (kg/km²) from trawl survey. *
 Plaice_eDNA_withoutlier: eDNA concentration for *Pleuronectes platessa*
 with outliers removed. * Sole_eDNA_withoutlier: eDNA concentration for
 *Solea solea* with outliers removed. * Sole_abundance: Estimated abundance
 of *Solea solea* (individuals/km²). * Plaice_abundance: Estimated
 abundance of *Pleuronectes platessa* (individuals/km²). #### File:
 Plaice_specificity.qlp **Description:** This file contains from
 quantitative assays used to validate the species-specificity of the eDNA
 assay targeting plaice. The `.qlp` file is a QuantaSoft Plate file
 generated using Bio-Rad QuantaSoft software. These files contain raw and
 processed droplet digital PCR (ddPCR) data associated with the experiments
 described in this dataset. #### File: Sole_specificity.qlp
 **Description:** This file contains from quantitative assays used to
 validate the species-specificity of the eDNA assay targeting sole. The
 `.qlp` file is a QuantaSoft Plate file generated using Bio-Rad QuantaSoft
 software. These files contain raw and processed droplet digital PCR
 (ddPCR) data associated with the experiments described in this dataset. ##
 Code/software All data are provided as CSV files, which can be opened and
 viewed using Excel or imported into the free, open-source R programming
 environment. The .qlp files were initially analyzed using Quantasoft
 software. Users who do not have access to QuantaSoft software are
 encouraged to use the  provided open-format files for data inspection,
 validation, and reuse. The `.qlp` files are included for completeness and
 reproducibility.