Estimating Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the Sacramento–San Joaquin River Delta

Abstract Juvenile Chinook salmon Oncorhynchus tshawytscha emigrating from natal tributaries of the Sacramento River must negotiate the Sacramento–San Joaquin River Delta, a complex network of natural and man-made channels linking the Sacramento River with San Francisco Bay. Natural processes and water management actions affect the fractions of the population using the different migration routes through the delta and survival within those routes. However, estimating these demographic parameters is difficult using traditional mark–recapture techniques, which depend on the physical recapture of fish (e.g., coded wire tags). Thus, our goals were to (1) develop a mark–recapture model to explicitly estimate the survival and migration route probabilities for each of four migration routes through the delta, (2) link these route-specific probabilities to population-level survival, and (3) apply this model to the first available acoustic telemetry data of smolt migration through the delta. The point estimate of survival through the delta for 64 tagged fish released in December 2006 (Ŝdelta = 0.351; SE = 0.101) was lower than that for 80 tagged fish released in January 2007 (Ŝdelta = 0.543; SE = 0.070). We attributed the observed difference in survival between releases to differences in survival for given migration routes and changes in the proportions of fish using the different routes. Our study shows how movements among, and survival within, migration routes interact to influence population-level survival through the delta. Thus, concurrent estimation of both route-specific migration and survival probabilities is critical to understanding the factors affecting population-level survival in a spatially complex environment such as the delta.