| Summary: | Abstract Background Imperfect detection of hard‐to‐sample organisms has motivated the development of novel monitoring techniques. Environmental DNA (eDNA) can provide a sensitive, relatively low‐cost sampling method in aquatic systems, but biotic and abiotic factors can affect its reliability. Aims We used a reintroduced population of radio‐tracked alligator snapping turtles (Macrochelys temminckii) to test the efficacy and ecology of eDNA in a lotic system. Materials & Methods We collected samples at turtle locations as well as random up‐ and downstream sites. Using a novel eDNA assay, we modeled occupancy and detection of eDNA using turtle biomass and remotely sensed UV exposure and also tested the relationship between these parameters and eDNA concentration. Results We found eDNA occupancy was best explained by upstream biomass and detection probability decreased with greater upstream UV exposure. The concentration of eDNA in a sample was not significantly affected by biomass measures, but decreased with higher upstream UV exposure, and the effect was significant. Discussion Our results show that UV exposure can affect aquatic eDNA sampling in situ with free‐ranging animals. The use of radiotelemetry allowed for higher control when modeling eDNA persistence and transport in a natural setting relative to laboratory, enclosure, or mesocosm studies. Conclusion We propose using wildlife tracking techniques to provide added realism to studies of eDNA dynamics.
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