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Manual of recommended practices for modelling physical – biological interactions during fish early life

The objectives of this manual of recommended practices (MRP) are to summarize appropriate methods for modelling physical – biological interactions during the early life of fish, to recommend modelling techniques in the context of specific applications, and to identify gaps in knowledge. This manual is intended to provide a reference for early‐career modellers who are interested in applying numerical models to fish early life and who would benefit from a summary of recommended practices for coupled biological – physical models that incorporate predictions from threedimensional circulation models to determine the transit of fish eggs, larvae, and juveniles from spawning to nursery areas. For current practitioners of numerical modelling in fish early life, the manual provides updates on latest techniques and areas in need of further research. Although the manual focuses on finfish, many of the summarized modelling techniques and recommended practices apply to modelling planktonic organisms, including zooplankton and other meroplankton (e.g. molluscs and crustaceans). It is important to recognize that “best” modelling practices depend upon the objective of the modelling exercise. In other words, no single model is appropriate to all applications. Instead, model formulations are situation‐specific. Because methodologies depend upon the goal of the endeavour, this manual includes an overview of basic components of fish early life models and presents recommendations in the context of three specific applications: adaptive sampling, connectivity, and recruitment prediction. The first three sections (Section 1 – Hydrodynamic models, Section 2 – Particle tracking, and Section 3 – Biological processes) summarize methodologies that are important components of three‐dimensional models of the early life of fish...