eDNA metabarcoding to monitor fish communities in a large river floodplain
Data files
Sep 24, 2025 version files 2.94 GB
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edna_env.csv
5.20 KB
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edna_lg_clean.csv
99.73 KB
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elec_env.csv
1.91 KB
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elec_long.csv
15.59 KB
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fish_codes.csv
5.07 KB
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raw_seq.zip
2.94 GB
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README.md
3.66 KB
Abstract
This dataset contains raw and processed environmental DNA (eDNA) metabarcoding and electrofishing data used to compare fish community composition across the floodplain of Lake St. Pierre, the largest floodplain habitat along the St. Lawrence River (Québec, Canada). The study aimed to evaluate the effectiveness of eDNA metabarcoding relative to traditional electrofishing for biomonitoring fish diversity in a hydrologically dynamic and heterogeneous floodplain system. Sampling was conducted across multiple floodplain sectors encompassing a gradient of land uses, from natural wetlands to annual crop agriculture.
The dataset includes: (1) raw Illumina sequence files from eDNA samples, (2) processed read tables generated following stringent bioinformatic filtering and taxonomic assignment, (3) site-level electrofishing catch data including species identity, abundance, and biomass, and (4) associated environmental metadata (e.g., sector, land use classification, geographic coordinates).
These data underpin analyses demonstrating that eDNA metabarcoding detects a broader range of species than electrofishing, while both methods reliably capture the most abundant taxa. The dataset further supports findings that eDNA-derived fish community composition is more strongly associated with spatial structuring across floodplain sectors than with variation in land use. The deposited files can be reused to explore species-specific detection patterns, method congruence, and spatial drivers of fish diversity in large river floodplains, and to inform future methodological comparisons in freshwater biomonitoring.
Dataset DOI: 10.5061/dryad.3bk3j9kzf
Description of the data and file structure
The data were collected as part of an experimental and field-based study comparing fish community composition assessed through environmental DNA (eDNA) metabarcoding and electrofishing surveys across a large river floodplain. Sampling included the collection of water samples for eDNA extraction and sequencing, concurrent electrofishing surveys for comparison, and the recording of environmental variables to evaluate potential drivers of community variation.
Files and variables
File: edna_env.csv
Description: Environmental variables associated with eDNA samples.
Variables
- station: Sampling sites code names
- year: Year of sampling
- landuse: Land use at the sampling sites
- manag: Land management at the sampling site
- region: Sector the sampling sites are located into
- Date: Sampling date
- UTM_X: UTM geographical cootdinates
- UTM_Y: UTM geographical cootdinates
- Turbidity: Water turbidity recorded at sampling site (FNU)
- Water_Level: Water level at each sampling site was modeled as the difference between GPS-derived altitude and modeled water level, with negative values indicating that water covered the site (i.e., water level above GPS altitude)
- Mean_NDVI: Mean Normalized Difference Vegetation Index (NDVI) values at each sampling site for the year preceding sampling
File: elec_env.csv
Description: Environmental variables associated with electrofishing samples.
Variables
- station: Sampling sites code names
- year: Year of sampling
- landuse: Land use at the sampling sites
- region: Sector the sampling sites are located into
- Date: Sampling date
- UTM_X: UTM geographical cootdinates
- UTM_Y: UTM geographical cootdinates
- Turbidity: Water turbidity recorded at sampling site (FNU)
- Water_Level: Water level at each sampling site was modeled as the difference between GPS-derived altitude and modeled water level, with negative values indicating that water covered the site (i.e., water level above GPS altitude).
- Mean_NDVI: Mean Normalized Difference Vegetation Index (NDVI) values at each sampling site for the year preceding sampling
File: edna_lg_clean.csv
Description: A long format fish abundance table derived from eDNA sampling after bioinformatic processing
Variables
- site: Sampling sites code names
- round: In 2022, two sampling rounds were conducted; this variable indicates the corresponding sampling round.
- region: Sector the sampling sites are located into
- landuse: Land use at the sampling sites
- year: Year of sampling
- CODE_BDRSI: Fish species codes
- count: Number of sequence
- rel_ab: Relative number of sequence at each site and dates
File: elec_long.csv
Description: A long format fish abundance table derived from electrofiching sampling
Variables
- station: Sampling sites code names
- year: Year of sampling
- CODE_BDRSI: Fish species codes
- count: Abundance
- rel_ab: Relative abundance at each site and dates
File: fish_codes.csv
Description: Species names associated with fish species codes
Variables
- Family:
- Genus:
- Species:
- CODE_BDRSI: Fish species codes
File: raw_seq.zip
Description: Raw sequences derived from Illumina sequencing. One forder for each sampling year. File names contain information as follows:
- 2019: filter-site code-year-marker_illumina ids_R1 or R2_001.fastq.gz
- 2022: marker-site code-round of samplingfilter_illumina ids_R1 or R2_001.fastq.gz