Animal populations are frequently infected by pathogens, but it is not always easy to determine the importance of pathogens to overall population dynamics. It is especially difficult to detect the effects of disease in population time series data because the effects are often local while overall population dynamics are also affected by larger-scale environmental factors. We overcame this difficulty by applying multivariate time series analysis to extract local effects from spawning abundance data and by comparing the survival rate of juvenile fall-run Chinook salmon Oncorhynchus tshawytscha from two locations in the Klamath River basin of California, one of which is affected by a high concentration of the myxozoan parasite Ceratomyxa shasta. To assess the effect of the disease (ceratomyxosis) caused by C. shasta on the population dynamics, we analyzed spatially structured abundance data for naturally spawning salmon and survival data for hatchery-released salmon for associations with exposure to C. shasta and stream discharge, another important factor with respect to ceratomyxosis in juvenile salmon. The results suggest that ceratomyxosis reduces the survival of the Chinook salmon that migrate through the location where parasite densities are highest and that this effect is also detectable in spawning abundance estimates.

The effects of an increased disease mortality rate on the transient and asymptotic dynamics of Chinook salmon (Oncorhynchus tshawytscha) were investigated. Disease-induced mortality of juvenile salmon has become a serious concern in recent years. However, the overall effects of disease mortality on the asymptotic and transient dynamics of adult spawning abundance are still largely unknown. We explored various scenarios with regard to the density-dependent process, the distribution of survivorship over the juvenile phase, the disease mortality rate, and the infusion of stray hatchery fish. Our results suggest that the sensitivity to the disease mortality rate of the equilibrium adult spawning abundance and resilience (asymptotic return rate toward this equilibrium following a small perturbation) varied widely and differently depending on the scenario. The resilience and coefficient of variation of adult spawning abundance following a large perturbation were consistent with each other under the scenarios investigated. We conclude that the increase in disease mortality likely has an effect on fishery yield under a fluctuating environment, not only because the mean equilibrium adult spawning abundance has likely been reduced, but also because the resilience has likely decreased and the variance in adult spawning abundance has likely increased. We also infer the importance of incorporating finer-scale spatiotemporal information into population models and demonstrate a means for doing so within a matrix population modeling framework.

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