Retrospective patterns of differential mortality and common year-effects experienced by spring and summer chinook salmon (Oncorhynchus tshawytscha) of the Columbia River

We used spawner–recruit data to estimate the instantaneous differential mortality (µ) experienced by seven Snake River spring and summer chinook (Oncorhynchus tshawytscha) stocks relative to six lower Columbia River stocks. We applied 37 Ricker stock–recruit models to these data, incorporating different assumptions about measurement error, transport survival, intrinsic productivity, methods of estimating µ, and common year-effects that affect the survival of all stocks. Estimates of mean µ for the 12 best models ranged from 0.55 to 1.90 (mean of 1.09), implying that passage from Lower Granite Dam to John Day Dam reduced recruitment of 1970–1990 Snake River broods by an average of 42–85% (mean of 66%). Differential mortality was cyclical and moderately high in the 1970s brood years, low for 1980–1983, near average in 1984–1989, and high in 1990. Our empirical estimates of µ showed low bias and were between those produced by two mechanistic passage models. The best empirical models included common year-effects, which shifted from generally positive effects on 1952–1968 brood years to generally negative effects on 1970–1990 broods. Year-effects were not significantly correlated with two climate indices or with water travel time (the time that water takes to travel down the Columbia River).