Migration routes and habitat use of a highly adaptable salmonid (sea trout, Salmo trutta) in a complex marine area

Abstract Background Understanding fish movements and migrations are paramount for management and conservation efforts. By applying Hidden Markov Models (HMMs) on records from electronic tags, migration routes of tagged fish can be reconstructed and new insights to the movement ecology of a species can be gained. We demonstrate the usability of HMMs on a widespread, iteroparous salmonid (sea trout, Salmo trutta) in a complex marine area with highly variable temperatures and salinities within small geographic distances. Understanding how the highly adaptable sea trout cope with these complex conditions could shed new light on factors driving the movement ecology of salmonids. Migration tracks of fish migrating at sea are reconstructed by applying an HMM on temperature and depth records from eight wild post-spawned sea trout from four Danish rivers. Results The fish migrated at sea for 47–142 days. Estimated positions of all fish were close to the coast (