Employing environmental DNA to evaluate invasive species removal and spatiotemporal dynamics of pupfish, crayfish, and Green Sunfish in a desert spring system

Dana Shellhorn

Aquatic invasive species disrupt ecosystem function and threaten native biodiversity through predation, competition, and habitat alteration. Eradication offers the best chance for ecosystem recovery but requires substantial time and resources, and detection of invasives at low densities is challenging. Environmental DNA (eDNA) sampling of genetic material shed by organisms into the environment provides a sensitive, cost-effective, and noninvasive alternative to traditional detection methods. In this study, we applied eDNA methods to inform invasive species eradication at Ash Meadows National Wildlife Refuge and explore spatiotemporal dynamics of endangered Ash Meadows Amargosa Pupfish (Cyprinodon nevadensis mionectes), and invasive Green Sunfish (Lepomis cyanellus), and Red Swamp Crayfish (Procambarus clarkii) in the target warm spring system. First, we quantified eDNA transport using a caged Green Sunfish experiment, then used these results to inform repeated eDNA sampling alongside traditional capture methods (gill nets, trap nets, electrofishing) to determine Green Sunfish distribution, target removal efforts, and evaluate eradication. Modeling indicated that collection of one sample every 160 m yielded >0.95 detection probability for 3 fish, while collection of 10 samples was required to reach the same detection probability for 1 fish (95% CI: 2–57). In field applications for eradication, eDNA detection was imperfect, but combining it with traditional sampling minimized false negatives, and eradication was completed in the targeted reach. Quantitative eDNA analysis of the three species revealed pupfish and crayfish DNA increased over time through the winter-spring season, likely in response to breeding activity rather than abundance changes. While no strong interactions were detected between crayfish and pupfish or Green Sunfish DNA, some evidence suggested a negative relationship between Green Sunfish and pupfish DNA, possibly reflecting habitat preference or predation by Green Sunfish. Green Sunfish DNA outside the target reach did not decrease over time despite additional control efforts, indicating more eradication is necessary. Otolith and stomach analyses confirmed Green Sunfish consumed pupfish but primarily fed on crayfish, aquatic snails and insects. All captured fish that could be aged were estimated to be 2–5 years old, indicating limited juvenile recruitment. System-wide eDNA sampling identified additional Green Sunfish strongholds for future eradication. Integrating eDNA with capture data and system knowledge proved effective for management-driven outcomes demonstrating the application of eDNA for investigating community ecology dynamics in desert spring systems and informing invasive species management and restoration at AMNWR and beyond.

Employing environmental DNA to evaluate invasive species removal and spatiotemporal dynamics of pupfish, crayfish, and Green Sunfish in a desert spring system

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