Estimating the effects of smolt size and migration timing on salmon marine survival using a multivariate mixed-effect model Journal of Applied Ecology

When the conditions encountered by a migratory species are highly variable, the timing of migration and migrant condition are critical to survival. Spring/summer-run Chinook salmon in the Snake River of the Northwestern United States are listed as threatened under the US Endangered Species Act because of decades of poor adult returns; juvenile smolt-to-adult survival is often 0.5% or less. Juveniles pass through eight dams en route to the ocean, and despite changes to the hydropower system, there has been little recent improvement in survival. We analysed the effect of migration date, fish length and their interaction on the survival to adulthood of 409,747 wild juvenile Chinook salmon as they migrated through a large, dynamic riverine ecosystem and through the ocean, measured over 20 years. Parametric 2D smoothers are often used to quantify unexplained heterogeneity across space; however, these same statistical models can be applied to 2D datasets to uncover patterns of covariance of two biological processes important to management actions. We employ Gaussian Markov random fields (GMRF) and a 2D smoother to estimates of fish survival to identify the nature of variation in survival with respect to length and date.