Estimating Cause‐Specific Mortality and Survival of Juvenile Fall Chinook Salmon: an Investigation of Avian Predation Across Large Spatial Scales

To investigate the effects of piscivorous colonial waterbird predation on juvenile salmonids (smolts) and to determine what proportion of all sources of smolt mortality was due to predation, we analyzed a data set describing fall Chinook Salmon Oncorhynchus tshawytscha that were marked with PIT tags in the Columbia River, USA. We used a state-space Bayesian model that incorporated live detections of tagged fish and recoveries of tags from dead fish to jointly estimate predation and survival over multiple river reaches and years (2008-2019). By incorporating recoveries of tags on bird colonies, the model was also able to increase the precision and spatial extent of survival estimates compared with a more traditional capture-recapture model. Results indicated that the avian predation probability (proportion of available fish consumed) varied depending on the predator species, colony location, and the fish's rearing type. Estimates of cumulative predation probability ranged annually from 0.066 (95% credible interval = 0.049-0.089) to 0.283 (0.210-0.419), and predation accounted for 7.3% (4.3-11.9%) to 29.1% (19.7-40.2%) of all sources of smolt mortality during out-migration to Bonneville Dam. Probabilities of predation on wild smolts were significantly higher than those for hatchery smolts in most river reaches and years. Predation probabilities were the highest for colonies of American white pelicans Pelecanus erythrorhynchos and double-crested cormorants Nannopterum auritum, which were located near where wild smolts rear and congregate. Estimates of predation by Caspian terns Hydroprogne caspia, California gulls Larus californicus, and ring-billed gulls L. delawarensis were often <0.03 of available smolts annually. Collectively, results indicated that the cumulative effects of predation on Chinook Salmon smolts were substantial in some but not all river reaches and years. Future models that consider biological and environmental factors influencing smolt susceptibility to avian predation may provide a more holistic understanding of the degree to which predation limits fish survival.