Assessing the efficacy of using a parentage-based tagging survival model to evaluate two sources of mortality for juvenile Chinook salmon (Oncorhynchus tshawytscha) in Lookout Point Reservoir, Oregon

We conducted a study to assess the efficacy of using a parentage-based tagging survival model (PBT N-mixture model) to evaluate two sources of mortality for juvenile Chinook salmon (Oncorhynchus tshawytscha) in Lookout Point Reservoir, Oregon. The model was originally developed to evaluate reservoir mortality because of predation from piscivorous fish. However, recent studies have also found that juvenile Chinook salmon experience high infection rates from parasitic copepods (Salmincola californiensis), which are known to negatively affect performance and survival. Our study was conducted to determine if the PBT N-mixture model could separately estimate mortality because of predation from non-native fish and mortality resulting from copepod infection. This assessment was conducted in two parts: (1) data collected in Lookout Point Reservoir during 2018 were re-analyzed; and (2) a simulation was conducted to evaluate a multi-year study that included inter-annual variation in copepod infection rate and two subsampling strategies (10 fish per month, 30 fish per month) to characterize monthly copepod infection rate. Results from each of these efforts suggest that the survival model is unlikely to provide reliable survival estimates for the two mortality sources that we evaluated. The re-analysis of 2018 data showed that “predation only” and “copepod only” models estimated a negative coefficient for the respective covariate, but the model that included both covariates provided coefficient estimates that differed from the other models and were highly uncertain. Similarly, the simulation results showed that most models failed to correctly estimate the magnitude and direction of mortality due to predation and copepods. These results suggest that additional data will be required if a model is desired that can separately estimate mortality effects due to both predation and copepods in the future. The existing data are limited by factors including low detection probabilities from previous field studies, existing uncertainties about copepod effects on mortality in a natural setting and expected limitations in the number of years that a field study could realistically be expected to receive funding.