Data for: Detection and quantification of two commercial flatfishes (Solea solea and Pleuronectes platessa) in the North Sea using environmental DNA
Data files
Feb 09, 2026 version files 60.86 MB
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AMK2020.csv
2.51 KB
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BTS2020.csv
2.65 KB
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BTS2021.csv
3.27 KB
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Mesocosm_plaice.csv
3.62 KB
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Mesocosm_sole.csv
832 B
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Plaice_specificity.qlp
8.23 MB
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README.md
7.60 KB
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Sole_specificity.qlp
52.61 MB
Abstract
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.
Dataset DOI: 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.
See the Material and Methods section of the associated publication.
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Maes, Sarah M.; Desmet, Sam; Brys, Rein et al. (2023). Detection and quantification of two commercial flatfishes (Solea solea and Pleuronectes platessa) in the North Sea using environmental
DNA . Environmental DNA. https://doi.org/10.1002/edn3.426