James T Thorson, Kasper Kristensen, Kerim H. Aydin, Sarah K Gaichas, David G. Kimmel, Elizabeth A. McHuron, Jens N. Nielsen, Howard Townsend, Andy Whitehouse

Mass-balance ecosystem models including Ecopath with Ecosim (EwE) are widely used tools for analyzing aquatic ecosystems to support strategic ecosystem-based management. These models are typically developed by first tuning unknown parameters to achieve mass balance (termed “Ecopath”), then projecting dynamics over time (“Ecosim”) while sometimes tuning predator-prey vulnerability parameters to optimize fit to available time-series. By contrast, population-dynamics (stock assessment) and multi-species models typically estimate a wide range of biological rates and parameters via their fit to time-series data, assess uncertainty via a statistical likelihood, and increasingly include process errors as “state-space models” to account for nonstationary dynamics and unmodeled ecosystem variables. Here, we introduce a state-space model “EcoState” (and associated R-package) that estimates parameters representing mass-balance dynamics directly via their fit to time-series data (absolute or relative abundance indices and fisheries catches) while also estimating the magnitude of process errors using RTMB. A case-study demonstration focused on Alaska pollock (Gadus chalcogrammus) in the eastern Bering Sea suggests that fluctuations in krill consumption are associated with cycles of increased and decreased pollock production. A self-test simulation experiment confirms that estimating process errors can improve estimates of productivity (growth and mortality) rates. Overall, we show that state-space mass-balance models can be fitted to time-series data (similar to surplus production stock assessment models), and can attribute time-varying productivity to both bottom-up and top-down drivers including the contribution of individual predator and prey interactions.