Hierarchical modeling of juvenile chinook salmon survival as a function of Sacramento-San Joaquin Delta water exports

1 A multi-year study in the Sacramento-San Joaquin Delta system was carried out to exam2 ine the relationship between the survival of out-migrating Chinook salmon Oncorhynchus 3 tshawytscha and the amount of water exported from the system by the two major pumping 4 stations in the southern portion of the Delta. Paired releases of groups of coded-wire-tagged 5 juvenile late-fall run Chinook salmon were made at two locations in the Delta, one in the 6 main stem Sacramento River and one in the interior portion of the Delta where they were 7 more likely to be directly affected by the pumping stations. Shortly after release, fish were 8 recovered downstream by a mid-water trawl, and, over a two to four year period, fish were 9 recovered in samples of ocean fishery catches and from spawning ground surveys. A Bayesian 10 hierarchical model for the recoveries was fit which explicitly accounted for between release 11 variation in survival and capture probabilities as well as sampling variation in the recoveries. 12 Survival of the interior Delta releases was considerably lower than the survival of main steam 13 releases (mean ratio of survival probabilities was 0.35). The ratio of survival probabilities 14 was negatively associated with water export levels, but various model selection criteria gave 15 more, or nearly equal, weight to simpler models which excluded exports. The signal-to-noise 16 ratio, as defined in terms of the export effect relative to environmental variation, however, 17 was very low, and could explain indeterminacy in the results of model selection procedures. 18 Many more years of data would be needed to more precisely estimate the export effect. 19 Whatever the factors are that adversely affect survival through the interior Delta, to deter20 mine the overall effect on out-migrating Sacramento river Chinook salmon the fraction of 21 out-migrants that enter the interior Delta needs to be estimated. 22