Fishery collapse, recovery, and the cryptic decline of wild salmon on a major California river

Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento–San Joaquin River system form the backbone of California’s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope (<jats:sup>87</jats:sup>Sr/<jats:sup>86</jats:sup>Sr) ratios of otoliths collected during carcass surveys from 2002 to 2010. Our results show that prior to the 2007–2008 salmon stock collapse, 55%–67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (∼90%) in 2011–2012. Though the rebound in abundance of salmon in the Feather River suggests recovery of the stock postcollapse, our otolith chemistry data document a persistent decline of wild spawners, likely leading to the erosion of locally adapted Feather River salmon populations.