Marine ecosystem models are used to investigate marine protected area (MPA) benefits for coral reef ecosystems located in Raja Ampat, in the heart of the Coral Triangle. Field data from an integrated and diverse research project is used to develop a spatial ecosystem model using Ecopath, Ecosim, and Ecospace modelling software. The ecological and fisheries responses of a reef ecosystem to different levels of fishing effort restrictions inside MPAs are explored. The trade-offs of allowing some fisheries to operate inside the MPAs versus designating the MPAs as no-take zones are highlighted. The results show that rapid rebuilding of reef fish populations, especially the large charismatic species, requires no-take areas. Distinct trade-offs in spillover benefits are observed between partially fished and no-take MPAs. 1. Introduction A global review of the status of coral reefs found that several coral reef ecosystems have declined; the review suggests that management for status quo is a “weak” goal; rather efforts should be made to restore the reefs [1]. Marine protected areas (MPAs) have been advocated to rebuild fish populations, mediate habitat damage, and preserve ecosystem biodiversity [2, 3]. Review of empirical results of the effects of marine reserves (i.e., no-take MPAs) shows that on average the density, biomass, diversity, and size of organisms are significantly higher inside the reserves [4]. Marine reserves appeared to promote an increased density of exploitable fishes in reef ecosystems in the Philippines [5, 6], the Caribbean [7, 8], and wherever they are adequately implemented and enforced [9]. Modelling studies have also demonstrated the biomass and spillover enhancing potential of reserves [10, 11]. The type of response depends on the species protected [12–14], location, size, spacing of protected areas [15], growth of tourism, diving operations [16], and other factors. Coral reefs are magnificent marine ecosystems; their incredible species richness and species composition play an important role in the ability of the ecosystems to respond to fishing and other stressors [17]. Fishing has resulted in changes to the target and nontarget reef fish communities [18–21]. Local abundances of coral reef fish are also determined by the relative magnitudes of larvae recruitment, colonization by juveniles and adults, predation, and competition for refuges [22]. Similar to the changes observed with fishing, recovery is also dependent on the competitive balance and trophic composition of reef ecosystems [23, 24]. A spatial ecosystem model of the coral
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