Development and application of individual-based models for predicting upstream passage of European fish

Anthropogenic alteration of rivers is ubiquitous and leads to fragmented river systems that restrict the passage of aquatic fauna. There are considerable efforts to facilitate unhindered migration through the installation of fish passage facilities. However, recent assessments suggest upstream passage efficiencies of 42%, and suggest that only 3% of rivers in Great Britain are fully connected. Decoding the behaviours that govern up-migrating fish responses to flow fields has been dubbed a high research priority that would allow for computational metrics of fish passage and a reduction in invasive experiments. The aim of this project was to develop cellular automata (CA), individual-based models (IBM), and computational fluid dynamic (CFD) models to predict the trajectories of up-migrating fishes and subsequently provide a method to computationally assess passage facilities. Past work was critically assessed to determine: the appropriate CFD approach to quantify the flow through various domains, the hydrodynamic stimuli that influence fish responses, and the current state of fish path prediction models and their applications and limitations. Multiple 2D CA and IBMs were developed to predict the passage efficiency of various eel tile configurations for juvenile European eels (Anguilla anguilla) using CFD-derived flow fields. Predictions compared well to a published values (76% vs. 74%) and suggested passage efficiency was highest for shallow slopes and low discharges. Results were extended to define maximum pass lengths and incorporated into an easy-to-use graphic. A 3D IBM, fishPy, was developed to predict up-migration trajectories of brown trout (Salmo trutta) based fish responses to hydraulic stimuli. Artificial hydrodynamic domains were created using CFD and used to verify model function. A CFD model of a passage facility on the River Esk was created based on collected bathymetry data, and compared well to measured velocity data. The IBM was applied to the passage facility and compared against measured passage metrics and fish trajectories. Overall, 2D and 3D models of up-migrating fishes were successfully developed and compared well to measured data. Potential areas for further research and development of the models are highlighted, including development of additional species modules for the 3D IBM.