Absolute fish population censuses in ponds demonstrate eDNA metabarcoding provides biodiversity estimates comparable to conventional sampling methods

Freshwater fishes are experiencing an unprecedented decline. Effective strategies for estimating the composition of fish communities are crucial for conservation efforts. While conventional physical collection methods can be effective, environmental DNA analysis has emerged as a potential alternative. Systematic comparisons of these methods are critical to evaluate their relative effectiveness. We collected water samples from 14 ponds near Hamilton, ON, which were analyzed for fish eDNA using two universal metabarcoding primers, and sampled using conventional methods (electrofishing and/or seining). A subset of ponds were then drained to obtain population census counts, facilitating a standardized comparison of false negatives and positives across conventional and eDNA sampling. We found no significant difference between survey methods in the number of species detected, although eDNA was more effective at detecting species at extremely low abundances, but was prone to false positives. W..., Metabarcoding data: Used the GenCatch Gel Extraction Kit and manufacturers protocol to prepare for reading on Thermofisher Ion Torrent at University of Windsor. Data included is raw data taken from this equipment before any of the data cleaning stages included in manuscript. 
eDNA samples: Collected from stormwater drainage ponds from/near Hamilton, ON in 2021 & 2022. Filtered water on-site through glass fiber filter and desicated with indicating silica beads. Transported to Windsor and kept at -20C until proccessed. DNA extracted in sterlile eDNA room at GLIER near University of Windsor. Used DNeasy kits following provided protocol for extraction, DNA was amplified using provided PCR conditions, then cleaned using Sera-Mag bead protocol with a final round of PCR using provided conditions. DNA was imaged on a 2% agarose gel to confirm successful amplification. Data includes location, start and end times, number of samples taken and IDs, basic environmental conditions, names of ..., , # Absolute fish population censuses in ponds demonstrate eDNA metabarcoding provides biodiversity estimates comparable to conventional sampling methods

[https://doi.org/10.5061/dryad.w9ghx3g07](https://doi.org/10.5061/dryad.w9ghx3g07)

## Description of the data and file structure

### I. General Information

Data collection dates: 2021 - 2023

Geographic location of data collection: Hamilton, ON, CA & Windsor, ON, CA

### Files and variables

### II. Data overview and methodological information

#### *File: Drained_Ponds_Raw_Data.csv*

**Date of creation: Feb 9, 2024**

The dataset contains 1 tab page. Empty cells indicate that a species was not detected at a specific size class within a pond. 

1. Pond_ID: Unique identifier for each pond that was drained. These IDs are used across all datasets. *Note* Pond 104 was sampled in two different years and was noted by either (2021) or (2022) next to the ID.
2. Forebay/Main Cell: Indicates whether the pond had a forebay that was drained to h...,