eDNA metabarcoding provides biodiversity estimates comparable to conventional sampling methods

Effective strategies for estimating the composition of fish communities are crucial for conservation efforts. While conventional specimen sampling methods can be effective, environmental DNA (eDNA) analysis has emerged as a potential alternative. However, systematic comparisons of these methods are critical to evaluate their relative effectiveness. We collected water samples from 14 ponds near Hamilton, ON, Canada, which were analyzed for fish eDNA using two universal metabarcoding primers. Surveyed ponds were also sampled using conventional fish sampling 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 sampling 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 (i.e., detection of fish eDNA in the absence of individuals collected during draining). We estimate that 11 eDNA samples should be sufficient to quantify fish community biodiversity in similar ecosystems. eDNA represents a viable alternative or complement to conventional methods, reinforcing its potential for enhancing aquatic ecosystem management.