Estimating Stage-Specific Survival and Abundance for Anadromous Salmonids Using the Multistate Emigration Model

Life cycle monitoring for anadromous salmonids is often aimed at estimating abundance of various life stages so that survival can be calculated in an ad hoc fashion as N(time 2) / N(time 1). Although unbiased capture-mark-recapture estimators for abundance are often used with sampling methods such as electrofishing (e.g., depletion) and trapping (e.g., DARR, Bjorkstedt 2005), difficulties with sampling methods can still lead to biases that may be outside the control of the practitioner (e.g., trap failure). There is also increasing evidence for transitions of individuals out of stream reaches of interest prior to the “typical” springtime smolt migration period that leads to estimates of apparent survival rather than true survival. A solution is to PIT-tag individuals as juveniles that are then subjected to detection on paired PIT antenna arrays operated year-round, as fish make their seaward migration and then again as fish move back into freshwater as adults to spawn. The multistate emigration model allows independent estimates of true survival, emigration and antenna detection efficiency. The model can be readily extended to incorporate data from counting weirs and individual and environmental covariates.