Representing species distributions in spatially-explicit ecosystem models from presence-only data

Spatially-explicit ecosystem models are increasingly considered for informing fisheries management. The inputs of these models that determine species distributions in the modeled system are critical. There is a need for methods to estimate species distributions in spatially-explicit ecosystem models from presence-only data. To address this need, we used a method relying on binomial generalized additive models integrating environmental covariates. This method allows for the production of distribution maps for ecosystem models such as Atlantis models, and of preference functions for Ecospace models; preference functions define the preferences of species groups for certain environmental parameter values and are employed by Ecospace to allocate species group biomasses spatially. The key step of the method we used is the objective generation of pseudo-absences for each month, by sampling with replacement the centroids of the cells of fine-scale spatial grids defined for each month. To demonstrate the method, we applied it to the diving bird and surface-feeding bird groups represented in the Atlantis model for the Gulf of Mexico (GOM), and to the seabird group represented in the Ecospace model for the West Florida Shelf. We also employed the distribution maps we constructed to provide a basis for a hypothetical marine protected area (MPA) planning scenario aiming to secure food for seabirds. Specifically, we produced a hotspot map for seabirds for the U.S. GOM from the distribution map of the species group, and then combined the hotspot map for seabirds with a hotspot map for their main prey, forage fish (Clupeidae and Exocoetidae), to determine where the hotspots of seabirds and forage fish overlap. This analysis suggested that, to secure forage fish for seabirds in the U.S. GOM, hypothetical MPAs should be implemented primarily within the coastal regions of the Louisiana-Texas shelf, within the coastal region of West Florida located between Sarasota and Naples and/or within Apalachee Bay, Florida.