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As climate stressors are impacting marine ecosystems and fisheries across the world, ecosystem models that incorporate environmental variables are increasingly used to inform ecosystem-based fisheries management. The assumptions around the mechanistic links between climate stressors and the biological processes in these models are important, but the implications for model outcomes of which stressors are captured and how they affect modeled biological processes are seldom explored. Using a whole-ecosystem model (Atlantis) for the Gulf of Alaska, we explore the effects of capturing physical (increased temperature) and biogeochemical (decreased low trophic level productivity) climate stressors, and disentangle the effects of each stressor on the productivity of forage fish, groundfish, and fish-eating seabirds. We then test the effects of alternative model specifications of temperature-driven habitat determination and bioenergetics. Increased temperature resulted in increased weight-at-age and higher natural mortality, while decreased productivity resulted in decreased weight-at-age and higher natural mortality. Model specification of temperature dependence of movement and spawning influenced model outcomes, and decoupling these processes from temperature led to overly optimistic biomass predictions. As the use of ecosystem models to inform fisheries management becomes more operational, we illustrate that the assumptions around the links between climate stressors and ecological processes influence model outcomes. [ABSTRACT FROM AUTHOR]

The availability of colonizable substrate is an important driver of the temporal dynamics of sessile invertebrates on coral reefs. Increased dominance of algae and, in some cases, sponges has been documented on many coral reefs around the world, but how these organisms benefit from non-colonized substrate on the reef is unclear. In this study, we described the temporal dynamics of benthic organisms on an Indonesian coral reef across two time periods between 2006 and 2017 (2006–2008 and 2014–2017), and investigated the effects of colonizable substrate on benthic cover of coral reef organisms at subsequent sampling events. In contrast with other Indonesian reefs where corals have been declining, corals were dominant and stable over time at this location (mean ± SE percentage cover 42.7 ± 1.9%). Percentage cover of turf algae and sponges showed larger interannual variability than corals and crustose coralline algae (CCA) (P < 0.001), indicating that these groups are more dynamic over short temporal scales. Bare substrate was a good predictor of turf cover in the following year (mean effect 0.2, 95% CI: 0–0.4). Algal cover combined with bare space was a good predictor of CCA cover the following year generally, and of sponge cover the following year but only at one of the three sites. These results indicate that turf algae on some Indonesian reefs can rapidly occupy free space when this becomes available, and that other benthic groups are probably not limited by the availability of bare substrate, but may overgrow already fouled substrates. [ABSTRACT FROM AUTHOR]