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

Abstract

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 (<5 trout per 50 linear m). We also showed that three replicate eDNA samples were sufficient to capture trout eDNA when eDNA was present. Although eDNA constitutes an effective addition to approaches to delimit the upper extent of fish, its effectiveness depends on previous knowledge of the last-fish boundary to apprise where to start sampling and targeting fish species anticipated to be last-fish. We present evidence that eDNA is a valuable tool in investigating fish distributions taking its place alongside traditional high-effort catch-release tools.

Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters

“…In some cases, traditional fish snorkeling can be more effective than eDNA, but this could be due to insufficient water volumes sampled, low densities of the target species, mobility of fish in lotic environments, and eDNA dilution from flowing water ( Ulibarri et al, 2017 ). In other cases, eDNA seems to be more effective in detecting the end of fish distribution in headwater streams than traditional electrofishing techniques ( Penaluna et al, 2021 ). Similarly, our study shows that eDNA has the potential to provide more positive detections of mud snails than traditional sampling.…”

“…Early detection of species in low numbers or that are elusive such as non-native species using eDNA is critical for managers to respond with the best strategy to prevent environmental degradation ( Pluess et al, 2012 ; Anglès d’Auriac et al., 2019 ; Penaluna et al, 2021 ). There are still many questions about best practices of using eDNA to detect invasive species in freshwaters.…”

“…eDNA provides an option for detection of species without physical capture or visual confirmation ( Davy, Kidd & Wilson, 2015 ). Due to rapid emergence of eDNA for detection of flora and fauna, it has generated interest among fisheries and other natural resource managers seeking cost-effective tools for aquatic species inventory and monitoring ( Pilliod et al, 2013 ; Coble et al, 2019 ; Penaluna et al, 2021 ).…”

Broad‐scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA

“…The often‐weaker headwater signals are suggestive of reduced densities and discontinuous habitat occupancy near the upstream extent of their distribution (cf. Penaluna et al ., 2021). Combinations of strong detections, weak detections and nondetections in proximity to eDNA sources are common in caged‐fish studies (Jane et al ., 2015; Robinson et al ., 2019; Thalinger et al ., 2021) and would be expected at the upstreammost extent of populations in which mixing of eDNA from target individuals throughout a river cross‐section is incomplete (Thalinger et al ., 2021; Wood et al ., 2020, 2021).…”

Development of a Quantitative PCR Assay for Four Salmon Species Inhabiting the Yangyangnamdae River Using Environmental DNA

“…This approach may also be used to estimate the abundance and biomass of fish species, which is represented by the eDNA concentration of each target species [ 39 , 40 , 41 ]. In fact, the abundance of eDNA exhibits a strong relationship to fish abundance recorded by traditional estimation surveys, such as mark–recapture sampling [ 42 ], electrofishing [ 43 , 44 ], and catch per unit effort using gillnet [ 45 ] or fyke nets [ 46 ]. In addition to its sensitivity and reliability, eDNA analysis has also been shown to be more energy and cost efficient than other methods used currently for salmon species [ 44 ].…”