Comparison of environmental DNA and underwater visual count surveys for detecting juvenile Coho Salmon in small rivers

ObjectiveThis study compares the probability of detecting juvenile Coho Salmon Oncorhynchus kisutch using both environmental DNA (eDNA) techniques and underwater visual count (UVC) surveys in northern California rivers. Here, UVC surveys commonly have detection probabilities (p) surpassing 0.90, providing an ideal setting to examine the performance of newer eDNA methods. We also evaluate the potential for using eDNA concentrations to predict the count of Coho Salmon within pool habitats.MethodsWe conducted paired eDNA and UVC surveys in 96 pools across 25 stream reaches within the Smith River basin, California. Method‐specific p and the effect of environmental covariates were estimated using multiscale occupancy modeling. We used generalized linear models to evaluate the relationship of fish counts to eDNA concentrations and habitat covariates.ResultThe eDNA and UVC methods showed a high degree of agreement in detecting the presence of Coho Salmon within a pool (93% agreement) and survey reach (80% agreement). Detection probabilities for eDNA (peDNA) and for UVC (pUVC) were similar and high at median levels of pool residual depth and contributing basin area (peDNA = 91%, pUVC = 89%). Contributing basin area (a proxy for discharge) had a strong, negative effect that was more pronounced for peDNA than for pUVC (e.g., in the largest basins, peDNA = 34% whereas pUVC = 77%). We did not find eDNA concentrations to be a good predictor of Coho Salmon counts in small pools.ConclusionThis study demonstrates that eDNA methods yielded nearly identical results to UVC surveys in catchments <36 km2 and can provide a highly effective approach for determining the distribution of Coho Salmon. However, additional investigation is required before eDNA could be used to estimate relative abundance in small pools.