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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.

Any fishery management scheme, such as individual fishing quotas (IFQs) or marine protected areas, should be designed to be robust to potential shifts in the biophysical system. Here we couple possible catch scenarios under an IFQ scheme with ocean acidification impacts on shelled benthos and plankton, using an Atlantis ecosystem model for the US West Coast. IFQ harvest scenarios alone, in most cases, did not have strong impacts on the food web, beyond the direct effects on harvested species. However, when we added the impacts of ocean acidification, the abundance of commercially important groundfish such as English sole ( Pleuronectes vetulus ), arrowtooth flounder ( Atheresthes stomias ), and yellowtail rockfish ( Sebastes flavidus ) declined up to 20%–80%, owing to the loss of shelled prey items from their diet. English sole exhibited a 10-fold decline in potential catch and economic yield when confronted with strong acidification impacts on shelled benthos. Therefore, it seems prudent to complement IFQs with careful consideration of potential global change effects such as acidification. Our analysis provides an example of how new ecosystem modeling tools that evaluate cumulative impacts can be integrated with established management reference points and decision mechanisms.

Leatherback turtles (Dermochelys coriacea) are critically endangered in the eastern and western Pacific Ocean. Here, I estimate the magnitude of two likely causes of their decline: (i) bycatch by longline fishing vessels and (ii) coastal sources of mortality. I calculate point estimates of longline bycatch based on turtle catch rates from the US Hawaii-based fleet and effort data for the international Pacific longline fleet. I estimate the intrinsic growth rate of the population and the magnitude of coastal mortality by fitting a simple logistic model. In the western and central Pacific, coastal sources lead to a 13% annual mortality rate, compared with a point estimate of 12% from longlining. In the eastern Pacific, coastal sources account for a 28% annual mortality rate, compared with a point estimate of only 5% from longlining. A Bayesian risk assessment reveals the importance of reducing coastal sources of mortality, as well as longline bycatch, if the populations are to avoid extinction. International efforts to protect the leatherback should expand beyond focusing solely on longline bycatch and should attempt to reduce coastal harvest of adult females and eggs, as well as reduce bycatch by inshore gears such as gillnets.

Commercial yield of tunas in the central Pacific increased severalfold between 1952 and 1998. We developed age-structured production models that incorporate information from multiple fisheries to estimate population biomass and recruitment trends of tunas (Thunnus alalunga, Thunnus albacares, Thunnus obesus, and Katsuwonus pelamis) and billfish in the central north Pacific (0°N to 40°N and 130°E to 150°W). Our results suggest that all tuna stocks remain above 40% of 1950s levels, whereas blue marlin (Makaira nigricans) declined to 21% and swordfish (Xiphias gladius) to 56%. Estimated biomasses of juvenile bigeye (T. obsesus) and yellowfin (T. albacares) tuna increased to 112 and 129%, respectively, of 1950s levels. Juvenile albacore (T. alalunga) decreased during the 1970s and 1980s but recovered to historical highs (121%) in recent years. Skipjack (K. pelamis) remained relatively stable between 1952 and 1980, declined by 35% between 1981 and 1990, and then increased to 68% of 1950s levels. These changes generally represent decreases in top predators and increases in small tunas, which make up their prey. Application of stock assessment methods set in a food web context provides an important step toward developing a method that recognizes fishery exploitation as a component of ecosystem dynamics.

Pelagic fisheries in the Pacific Ocean target both large (Thunnus spp.) and small tunas (juveniles of Thunnus spp; Katsuwonus pelamis) but also take billfishes (Xiphias gladius, Makaira spp., Tetrapturus spp., Istiophorus platypterus) and sharks (Prionace glauca, Alopias superciliosus, Isurus oxyrinchus, Carcharhinus longimanus, Galeocerdo cuvieri) as bycatch. We developed a multispecies model using the Ecopath with Ecosim software that incorporated time-series estimates of biomass, fishing mortality, and bycatch rates (1952–1998) to evaluate the relative contributions of fishing and trophic impacts on tuna dynamics in the central Pacific (0°N to 40°N and 130°E to 150°W). The Ecosim model reproduced the observed trends in abundance indices and biomass estimates for most large tunas and billfishes. A decline in predation mortality owing to depletion of large predators was greatest for small yellowfin tuna and could possibly account for apparent increases in biomass. For other tunas, however, predicted changes in predation mortality rates were small (small bigeye) or were overwhelmed by much larger increases in fishing mortality (skipjack and small albacore). Limited evidence of trophic impacts associated with declining apex predator abundance likely results from the difficulties of applying detailed trophic models to open ocean systems in which ecological and fishery data uncertainties are large.