In streams, chemical piscicides can be an effective tool for eradication of invasive fish. However, chemical treatments are expensive, time consuming, and do not discriminate between invasive and native species in a system. To reduce project costs and biological impacts to the native community, an eradication project ideally would treat the entire area occupied by the non-native species, avoid areas where non-native species are absent, and eliminate all target individuals in one treatment. Highly sensitive methods for detecting animals in low abundance are needed to support this careful targeting.
We studied how environmental DNA (eDNA) sampling addressed these challenges through three case studies, each of which used eDNA sampling to inform removal of Brook Trout (Salvelinus fontinalis) in small streams. We found that eDNA methods can be informative throughout all stages of eradication projects in stream settings. They can assist with delimiting the population prior to treatment, provide detailed location data on surviving target individuals, and serve as an efficient and relatively inexpensive monitoring tool to assess long-term treatment efficacy. When combined with traditional survey tools, such as electrofishing, eDNA sampling may help reduce the size and number of treatments necessary to reach project goals. This translates directly to increased efficacy of treatments, reduced labor and cost, and reduced impact on native species.