Viability of high-frequency environmental DNA (eDNA) sampling as a fish enumeration tool

Abstract

Despite growing interest in environmental DNA (eDNA) monitoring as a low-cost, non-invasive tool for monitoring fish presence and relative abundance, quantitative comparisons between fish abundance and eDNA are still rare, especially for anadromous species of conservation concern. To examine the relationship between eDNA data and management-relevant abundance data, we assessed eDNA abundance of river herring, an ecologically relevant anadromous sister-species pair, alongside sonar-generated fish counts at a well-characterized site in the Choptank River, Chesapeake Bay, MD. Over the 2021 spawning season, there was a strong correlation between daily eDNA concentration and daily counts of fish swimming upstream (Spearman’s rho = 0.86). A generalized additive model for location scale and shape (GAMLSS) was used to estimate fish count as a function of flow-corrected eDNA concentration and relevant covariates. Model- and sonar-generated run counts were 729,385 and 733,208 fish respectively, differing by just 0.5 %. A sub-sampling analysis showed that a model built on at least five weeks of data could utilize eDNA abundance to produce accurate estimates for the remainder of the season, while a reduction in eDNA sampling frequency substantially reduced run count accuracy. This work emphasizes the utility of quantitative eDNA monitoring for river herring populations and shows the necessity of high-frequency eDNA sampling to estimate run count.