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We describe and document an end-to-end model of anchovy and sardine population dynamics in the California Current as a proof of principle that such coupled models can be developed and implemented. The end-to-end model is 3-dimensional, time-varying, and multispecies, and consists of four coupled submodels: hydrodynamics, Eulerian nutrient–phytoplankton–zooplankton (NPZ), an individual-based full life cycle anchovy and sardine submodel, and an agent-based fishing fleet submodel. A predator roughly mimicking albacore was included as individuals that consumed anchovy and sardine. All submodels were coded within the ROMS open-source community model, and used the same resolution spatial grid and were all solved simultaneously to allow for possible feedbacks among the submodels. We used a super-individual approach and solved the coupled models on a distributed memory parallel computer, both of which created challenging but resolvable bookkeeping challenges. The anchovy and sardine growth, mortality, reproduction, and movement, and the fishing fleet submodel, were each calibrated using simplified grids before being inserted into the full end-to-end model. An historical simulation of 1959–2008 was performed, and the latter 45 years analyzed. Sea surface height (SSH) and sea surface temperature (SST) for the historical simulation showed strong horizontal gradients and multi-year scale temporal oscillations related to various climate indices (PDO, NPGO), and both showed responses to ENSO variability. Simulated total phytoplankton was lower during strong El Nino events and higher for the strong 1999 La Nina event. The three zooplankton groups generally corresponded to the spatial and temporal variation in simulated total phytoplankton. Simulated biomasses of anchovy and sardine were within the historical range of observed biomasses but predicted biomasses showed much less inter-annual variation. Anomalies of annual biomasses of anchovy and sardine showed a switch in the mid-1990s from anchovy to sardine dominance. Simulated averaged weights- and lengths-at-age did not vary much across decades, and movement patterns showed anchovy located close to the coast while sardine were more dispersed and farther offshore. Albacore predation on anchovy and sardine was concentrated near the coast in two pockets near the Monterey Bay area and equatorward of Cape Mendocino. Predation mortality from fishing boats was concentrated where sardine age-1 and older individuals were located close to one of the five ports. We demonstrated that it is feasible to perform multi-decadal simulations of a fully-coupled end-to-end model, and that this can be done for a model that follows individual fish and boats on the same 3-dimensional grid as the hydrodynamics. Our focus here was on proof of principle and our results showed that we solved the major technical, bookkeeping, and computational issues. We discuss the next steps to increase computational speed and to include important biological differences between anchovy and sardine. In a companion paper (Fiechter et al., 2015), we further analyze the historical simulation in the context of the various hypotheses that have been proposed to explain the sardine and anchovy cycles.

In 1989–90 the small pelagic fishery of the Gulf of California began to show a very marked decline in the catch of its main component, the Pacific sardine (Sardinops sagax). The catch plummeted from 292,000 t in 1988–89 to 7000 t in 1991–92 and 1992–93. This caused a serious economic crisis in the local fishery fleet and industry, and resulted in the loss of 3000 jobs. In 1993–94 the fishery showed signs of recovery as the abundance of the Pacific sardine began to recover. The catch improved to 128,000 t in 1993–94 and further to 215,000 t in 1996–97. In trying to understand this great variability, we proposed the hypothesis that the distribution and the abundance of the Pacific sardine of the Gulf of California is determined by the wind patterns (upwelling) and the sea surface temperature. The results of analyzing data from 25 cruises showed the period of low relative abundance between 1990 and 1993 and one of high abundance between 1993 and 1996. The range of the sardine's distribution expanded as its abundance increased and contracted when abundances were low. The relationship between the abundances of the sardine and environmental variables proved to nonlinear and bell-shaped. The adjusted pattern explained 78.8% of the variability of the sardine abundance. The highest abundance are produced by moderate upwelling (13–18 m3s−1 per 10 m of coastline) and sea surface temperatures of between 19°C and 25°C.