Better boundaries: identifying the upper extent of fish distributions in forested streams using eDNA and electrofishing

Publications Type: 
Journal Article
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Penaluna, Brooke E.; Allen, Jennifer M.; Arismendi, Ivan; Levi, Taal; Garcia, Tiffany S.; Walter, Jason K. 2021. Better boundaries: identifying the upper extent of fish distributions in forested streams using eDNA and electrofishing. Ecosphere. 12(1): e03332. doi:


The management of species that occur in low densities is a conservation concern worldwide across taxa with consequences for managers and policymakers. The distribution boundary at the upper extent of fish in North America receives extra attention because stream reaches with fish are managed differently and often have more protections than fishless reaches. Here, we examine the relative reliability of water environmental DNA (eDNA), polymerase chain reaction (PCR)-amplified for Coastal Cutthroat Trout (Oncorhynchus clarkii clarkii) to detect the upper extent of fish across streams as a potential management tool compared to standard electrofishing methods. We provide estimates of fish detection probabilities from eDNA analyses, and probabilities of detection for both eDNA field samples and quantitative PCR (qPCR) given covariates of habitat characteristics and fish densities from electrofishing. We present a primer and probe based on the cytochrome oxidase I gene using qPCR to detect trout DNA across water samples from 60 forested streams in the Pacific Northwest, USA using high-resolution spatial sampling. In 28% of streams, the upper extent of fish matches between methods. In over half of the streams, Coastal Cutthroat Trout eDNA was detected above the electrofishing last-fish boundary. Although some detections could be attributed to false-positive errors, eDNA results extend the upstream, leading edge of fish by 50?250 m from the electrofishing boundary. In 20% of the streams, detections of last-fish occurred higher in the stream network with electrofishing rather than eDNA, but generally by only 50 m. Modeled results revealed that the occurrence of trout eDNA was higher in wider-stream locations and that eDNA detections occurred at lower electrofishing densities (