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Efforts to understand causes of declines in productivity of species of concern often involve retrospective evaluation of multiple possible causes based on trends in relevant ecological indicators. We describe a hypothesis testing framework for examining declines in marine survival for coho and Chinook salmon in the Salish Sea. Independent populations of both anadromous species have declined over the last 50 years, prompting extensive examination of mortality in different life stages. Previous studies have identified declining trends in marine survival, and we re-evaluated these trends in light of a number of possible hypotheses for declines. We laid out seven potential explanations for declines: changes in predator buffering related to abundance and timing, density-dependent or -independent food availability, water quality, timing of freshwater delivery to Puget Sound, and anthropogenic impacts. We compiled ecosystem indicators relevant to these hypotheses and used generalized additive models (GAMs) to examine multivariate relationships with survival from multiple coho and Chinook salmon stocks. We also developed additional models using the most informative indicators based on variable importance weighting (VIW) from the seven hypothesis groups. We examined how these models explained overall trends in marine survival, as well as survival in three temporal stanzas (before, during, and after a major decline, based on statistical breakpoint analysis). Across the entire time series, best fitting models explained 30–40% of the variation in the survival data. Best fitting models were from multiple hypotheses, including predation (abundance and timing), competition, water quality, and anthropogenic impacts; the freshwater delivery hypothesis was the least supported. Different models performed best (lowest error) during different stanzas of the coho salmon marine survival time series and the two VIW models were generally the top performing models, but performance varied in different years. Indicators with the strongest support included seal abundance, herring abundance, timing of hatchery salmon releases, and indicators related to water properties like stratification and temperature. These findings suggest that multiple processes embedded in several of our hypotheses influence marine survival but that an ecological “smoking gun” for Salish Sea salmon declines will remain elusive.

Identifying factors that influence anadromous Pacific salmon (Oncorhynchus spp.) population dynamics is complicated by their diverse life histories and large geographic range. Over the last several decades, Chinook salmon (O. tshawytscha) populations from coastal areas and the Salish Sea have exhibited substantial variability in abundance. In some cases, populations within the Salish Sea have experienced persistent declines that have not rebounded. We analyzed a time series of early marine survival from 36 hatchery Chinook salmon populations spanning ocean entry years 1980–2008 to quantify spatial and temporal coherence in survival. Overall, we observed higher inter-population variability in survival for Salish Sea populations than non-Salish Sea populations. Annual survival patterns of Salish Sea populations covaried over smaller spatial scales and exhibited less synchrony among proximate populations relative to non-Salish Sea populations. These results were supported by multivariate autoregressive state space (MARSS) models which predominantly identified region-scale differences in survival trends between northern coastal, southern coastal, Strait of Georgia, and Puget Sound population groupings. Furthermore, Dynamic Factor Analysis (DFA) of regional survival trends showed that survival of southern coastal populations was associated with the North Pacific Gyre Oscillation, a large-scale ocean circulation pattern, whereas survival of Salish Sea populations was not. In summary, this study demonstrates that survival patterns in Chinook salmon are likely determined by a complex hierarchy of processes operating across a broad range in spatial and temporal scales, presenting challenges to the management of mixed-stock fisheries.