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Management of protected species is difficult when objectives include the recovery of both predator and its prey. Ideally, identifying trade-offs between competing objectives involves evaluating management alternatives with a quantitative model that integrates information on both species, but data are often limited. We used new predator diet data and simulation modeling to update our understanding of seal predation on juvenile Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) in the Puget Sound. Under prey size assumptions used by previous studies, estimates suggest predation could be a significant source of mortality for Chinook salmon (mean: 37% of ocean age-0 juveniles), but varied considerably among years (range of median estimates: 22%–49%). However, when we estimated prey size from otoliths recovered from seal scats, the impact (numbers of fish consumed) decreased by 71%. Predation on coho salmon was estimated to be relatively low under both scenarios (6%–8% of ocean age-0 juveniles) with a 21% decrease in consumption using otolith-derived prey size. Our analysis highlights the importance of updating model inputs and re-evaluating assumptions of multi-species models used for ecosystem-based fisheries management.

Conflicts can arise when the recovery of one protected species limits the recovery of another through competition or predation. The recovery of many marine mammal populations on the west coast of the United States has been viewed as a success; however, within Puget Sound in Washington State, the increased abundance of three protected pinniped species may be adversely affecting the recovery of threatened Chinook salmon (Oncorhynchus tshawytscha) and endangered killer whales (Orcinus orca) within the region. Between 1970 and 2015, we estimate that the annual biomass of Chinook salmon consumed by pinnipeds has increased from 68 to 625 metric tons. Converting juvenile Chinook salmon into adult equivalents, we found that by 2015, pinnipeds consumed double that of resident killer whales and six times greater than the combined commercial and recreational catches. We demonstrate the importance of interspecific interactions when evaluating species recovery. As more protected species respond positively to recovery efforts, managers should attempt to evaluate tradeoffs between these recovery efforts and the unintended ecosystem consequences of predation and competition on other protected species.

Knowing the species and life stages of prey that predators consume is important for understanding the impacts that predation may have on prey populations, but traditional methods for determining diets often cannot provide sufficient detail. We combined data from two methods of scat analysis (DNA metabarcoding and morphological prey ID) to quantify the species and life stages of salmon (Oncorhynchus spp.) consumed by harbour seals (Phoca vitulina) in the Strait of Georgia, Canada, where juvenile Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon survival is poor. Harbour seals primarily consumed adult salmon of lesser conservation concern in the fall (August–November): chum (Oncorhynchus keta: 18.4%), pink (Oncorhynchus gorbuscha: 12.6%), sockeye (Oncorhynchus nerka: 7.4%), Chinook (7.1%), and coho (1.8%). However, the opposite species trend occurred during the spring when seals preferred juvenile salmon of greater conservation concern (April–July): coho (2.9%), Chinook (2.9%), sockeye (2.5%), pink (1.4%), and chum (0.8%) — percentages that can equate to many individuals consumed. Our data suggest that harbour seals select juveniles of salmon species that out-migrate at ages >1 year and provide evidence of a potential causal relationship between harbour seal predation and juvenile salmon survival trends.