Occupancy Modeling of eDNA from an Endangered Darter in Turbid Rivers

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Many imperiled freshwater organisms are difficult to detect, and potentially negatively affected, by traditional sampling techniques. The environmental DNA (eDNA) approach to aquatic species surveys promises low invasiveness and high detection rates, but the robustness of this technique to large stream-size, persistent turbidity, and a rich, closely-related fauna have been poorly investigated. We developed an eDNA monitoring protocol for endangered Roanoke logperch (Percina rex ), a darter endemic to the darter-rich Roanoke, Dan, and Nottoway basins. Detection and occupancy rates of eDNA, and their sensitivity to biotic and abiotic covariates, were estimated in an occupancy model framework. Our quantitative PCR (qPCR) assay reliably amplified Roanoke logperch DNA, but not the DNA of co-occurring taxa, and water samples from four presumed-unoccupied rivers were always negative for eDNA. In contrast, Roanoke logperch eDNA was detected at 11 of 12 sites (in 53 of 96 water samples) in rivers presumed occupied by the species. These sites spanned a wide range of stream-sizes, physiographies, water chemistries, and turbidities (mean 8 NTU; range 1-16 NTU), but none of these factors appreciably influenced eDNA detection. Rather, based on occupancy models, eDNA detection and occupancy rates were strongly influenced by Roanoke logperch density at the site, estimated from previous electrofishing surveys. Our estimated detection probability per water sample ranged from 0.55 to 0.82 among sites. Based on these estimates and the collection of eight water samples per site, the false-negative probability (i.e., failing to detect Roanoke logperch when it occurs) was less than 0.003, an efficiency unrivaled by traditional sampling techniques. The reliability and ease of implementation of this technique should allow for rapid surveys of Roanoke logperch presence/absence, a prerequisite for informed management decisions. We therefore recommend eDNA as a useful tool to monitor the distribution of this and potentially other cryptic aquatic species.


Georgia Chapter of the American Fisheries Society Annual Meeting (GA-AFS)


Statesboro, GA