High replicability in strong correlation between goldfish abundance, eDNA detection probability, and eDNA concentration in urban ponds
Data files
May 27, 2026 version files 131.84 KB
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CPUE_Data.csv
10.82 KB
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Depletion_totalabun.csv
2.50 KB
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DFO_qPCR_data.csv
42.27 KB
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Fish_Dat.csv
46.59 KB
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GLIER_eDNA_concentrations_with_HAM_sample_code.csv
5.28 KB
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Pond_Data.csv
338 B
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R_Code.R
18.96 KB
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README.md
5.08 KB
Abstract
Goldfish (Carassius auratus) is a globally invasive species commonly found in urban environments due to releases associated with the aquarium trade. Environmental DNA (eDNA) represents a novel, cost-efficient, and sensitive technique to indirectly detect aquatic organisms by analyzing residual genetic material in environmental samples. We utilized eDNA to monitor invasive goldfish in 29 urban ponds near Hamilton, Ontario, evaluating both detection sensitivity of eDNA in comparison to conventional fisheries survey methods (electrofishing and seining) and the quantitative relationship between eDNA concentration and population abundance and biomass, determined from population censuses obtained following complete draining of eight ponds. This dataset includes the fisheries data generated from all urban stormwater ponds, the qPCR data generated from the eDNA samples collected from each pond, and the R code used to analyze these data.
Dataset DOI: 10.5061/dryad.bvq83bkp0
Description of the data and file structure
Urban stormwater management ponds in Hamilton, Ontario, Canada, were surveyed using both conventional fisheries methods and eDNA methods to compare relationships between invasive goldfish abundance, eDNA detection probability, and eDNA concentrations. Conventional fisheries methods used include electrofishing, seining, and pond draining (after which complete census counts were taken). Environmental DNA samples were collected, extracted, and analyzed by two independent working groups (GLIER and DFO). Environmental DNA detection and concentrations were estimated using quantitative PCR.
Files and variables
File: CPUE_Data.csv
Description:
Variables
- Pond ID: Pond Name
- Species: The species captured
- Cell: Whether the pond cell was the main cell or 'forebay'
- Pond size m2: Pond size, in square meters
- Total captured: Total fish captured
- Seine Size_Sqm: The size of the seine deployed
- Capture_method: Whether fish were captured using electrofishing or seining
- Seine/efish #: The number of seine or electrofishing passes made on the pond
- total efish minutes: Total minutes electrofished
- CPUE (seine) m2 : The catch-per-unit effort for seining
- CPUE (efish) fish/minute: The catch-per-unit-effort for electrofishing
- Month: The month the survey was conducted
- Year: The year the survey was conducted
File: Depletion_totalabun.csv
Description:
Variables
- Pond_ID: The name of the pond surveyed
- Forebay/Main Cell: Whether the main cell or 'forebay' of the pond was surveyed
- Species: The specied captured
- YOY1: The number of size class YOY1 individuals captured
- YOY2: The number of size class YOY2 individuals captured
- YOY3: The number of size class YOY3 individuals captured
- Adult1: The number of size class Adult1 individuals captured
- Adult2: The number of size class Adult1 individuals captured
- Adult3: The number of size class Adult1 individuals captured
- Adult4: The number of size class Adult1 individuals captured
- Adult5: The number of size class Adult1 individuals captured
- Adult6: The number of size class Adult1 individuals captured
- Not specified: Numbers of individuals for which size class data were not specified
- Total count by Species: Total individuals of a species captured
- Date: Date the survey was conducted
- Comments: Additional notes
File: DFO_qPCR_data.csv
Description:
Variables
- Year: Year the sample was collected
- Pond: The name of the pond the sample was collected from
- Month: The month the sample was collected
- Sample: The sample ID
- Reps-amplified: The number of technical replicates that amplified
- Ct-mean: The mean Ct value across technical replicates for the sample
- Ct-SD: The standard deviation of the Ct value of the technical replicates for the sample
- Quantity.mean: The average estimated concentration of each sample across technical replicates
- Quantity-SD: The standard deviation of the concentration of each sample across technical replicates
- Goldfish-expected: Whether goldfish were expected to be detected
- Copies.L: The concentration (copies/L) of eDNA in the environmental sample
File: Fish_Dat.csv
Description:
Variables
- Date Collected: Date the individual was collected
- Location: The pond from which the individual was collected
- FL_mm: The fork length of the individual, in millimeters
- Weight_g: The mass of the individual, in grams
- Size.class: The size class to which the individual was assigned
- Alternative.mean: Data used as a 'proxy' for when individual-level data did not exist for a specific size class from a pond
File: GLIER_eDNA_concentrations_with_HAM_sample_code.csv
Description:
Variables
- FWI ID: The matching sample ID of the DFO sample collected from the sample location
- Quantity Mean: The quantity of eDNA estimated in each sample by the GLIER working group, averaged across technical replicates
- Quantity SD: The standard deviation of the concentration estimates generated by teh GLIER working group, averaged across technical replicates
File: Pond_Data.csv
Description:
Variables
- Pond: The name of the pond
- Surface.Area (hectare): The surface area of the pond, in hectares
- Surface.Area (sqf): The surface area of the pond, in square feet
- Perimeter (m): The length of the perimeter of the pond
File: R_Code.R
Description: The R code used to analyze the above datafiles.
Code/software
All data are uploaded in .csv files; standard programs to view .csv files can be used to access the data (microsoft excel, libre office, etc.).
The statistical software 'R' was used to analyze all data.
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA