Environmental DNA Sampling Identifies Different Nonnative and Native Salmonid Species Assemblages in Two Eastern Oregon Wilderness Areas

Wilderness areas often provide critical habitat for native fishes. However, the remoteness of wilderness areas can limit fish monitoring efforts, such that changes in nonnative and native fish distributions may not be detected and management responses may be delayed. Environmental DNA (eDNA) sampling offers a non-invasive and efficient method to monitor aquatic species across remote waterways. We used eDNA sampling and species-specific qPCR analysis to assess distributions of nonnative brook trout (Salvelinus fontinalis) and native bull trout (S. confluentus) and Columbia River redband trout (Oncorhynchus mykiss gairdneri) across sections of Monument Rock and Strawberry Mountain Wilderness Areas in eastern Oregon. In Monument Rock, we did not detect brook trout or bull trout eDNA, supporting previous findings of brook trout non-invasion and bull trout extirpation. Redband trout eDNA was detected at 29 of 34 Monument Rock sites despite recent environmental disturbances. Environmental DNA from all species was detected in Strawberry Mountain. Brook trout eDNA was detected at 10 of 17 Strawberry Mountain sites, indicating upstream expansion of this nonnative species in Meadow Fork Big Creek. Bull trout eDNA was detected at seven sites and redband trout eDNA was detected at four sites, confirming native salmonid persistence despite decades of co-occurrence with brook trout. Brook trout eDNA concentrations were highest in samples closer to High Lake where the species was first introduced, while native salmonid eDNA concentrations were higher at locations further from the lake. This study provides baseline distributions for these species and a framework for using eDNA sampling to monitor fish distributions in remote areas. Key Points We found that native salmonids are using habitat within Monument Rock and Strawberry Mountain Wilderness Areas. However, habitat degradation and expanding nonnative species may limit wilderness benefits to native salmonids in Monument Rock and Strawberry Mountain Wilderness Areas, respectively. This study provides a framework for using environmental DNA sampling to efficiently monitor fish distributions in remote waterways and to inform future management actions.