A Multi-State Capture-Recapture Modeling Strategy to Separate True Survival from Permanent Emigration for a PIT-Tagged Population of Stream Fish

Robust estimates of survival and movement are important for informing the recovery of fish populations as well as the study of life history, behavior and population ecology.  We present a multi-state capture-recapture model that allows separate and simultaneous estimates of true survival and fidelity to the study reach in the face of imperfect recapture and detection probabilities.  The key study design element that permitted this separation was the use of a multiple passive integrated transponder (PIT) tag antenna array to detect PIT-tagged individuals as they emigrated from the study area.  The modeling approach incorporated live-recapture data during discrete sampling occasions with observational data on antenna detections of tagged individuals as they exited the study area between sampling occasions.  The multi-state emigration model was applied to empirical data from a stream-dwelling, PIT-tagged cohort of Atlantic salmon (Salmo salar) for which emigration was continuously monitored using a pair of stationary PIT tag antennas.  The study design we outline presents a way to inform key management, recovery and ecological questions.  Our analysis showed how estimates of the joint probability of surviving and remaining faithful to the study reach (apparent survival) that are based solely on live recapture data (e.g., from the Cormack-Jolly-Seber model) masked the patterns revealed from separately estimating true survival and emigration using the multi-state emigration model.  Because the multi-state model was used as a basis, we were also able to consider size-dependence in survival and emigration in a straightforward way; the estimated size-dependent functions support hypotheses regarding the mechanisms leading to survival and/or emigration responses of Atlantic salmon and other stream-dwelling salmonids.