Evaluation of long-term mark-recapture data for estimating abundance of juvenile fall-run Chinook salmon on the Stanislaus River from 1996 to 2017

This paper used 21 years of mark-recapture data and rotary screw trap catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. The authors compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, they observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, and abundance trends from year to year did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method.