Embedding stock assessment within an integrated hierarchical Bayesian life cycle modelling framework : an application to Atlantic salmon in the Northeast Atlantic

• Published in: ICES Journal of Marine Science
• Main Authors: Massiot-Granier, Félix, Prévost, Etienne, Chaput, Gerald, Potter, Ted, Smith, Gordon, White, Jonathan, Mäntyniemi, Samu, Rivot, Etienne
• Other Authors: Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Fisheries and Oceans Canada (DFO), Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science Weymouth (CEFAS), Inchbraoch House, Marine Scotland, Fisheries Science Services, Marine Institute, Fisheries and Environmental Management Group, The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007– 2013) under grant agreement No. 244706/ECOKNOWS project
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2014
• Subjects: atlantic salmon; complex of populations; stock assessment; hierarchical bayesian model; integrated life cycle; mixed stock fishery; north atlantic; prefishery abundance; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Greenland; Atlantic salmon; Faroes; North Atlantic; Northeast Atlantic
• Online Access: https://hal.archives-ouvertes.fr/hal-01210198; https://doi.org/10.1093/icesjms/fst240

International audience We developed a hierarchical Bayesian integrated life cycle model for Atlantic salmon that improves on the stock assessment approach currently used by ICES and provides some interesting insights about the population dynamics of a stock assemblage. The model is applied to the salmon stocks in eastern Scotland. It assimilates a 40-year (1971–2010) time-series of data compiled by ICES, including the catches in the distant water fisheries at Faroes and West Greenland and estimates of returning fish abundance. Our model offers major improvements in terms of statistical methodology for A. salmon stock assessment. Uncertainty about inferences is readily quantified in the form of Bayesian posterior distributions for parameters and abundance at all life stages, and the model could be adapted to provide projections based on the uncertainty derived from the estimation phase. The approach offers flexibility to improve the ecological realism of the model. It allows the introduction of density dependence in the egg-to-smolt transition, which is not considered in the current ICES assessment method. The results show that this modifies the inferences on the temporal dynamics of the post-smolt marine survival. In particular, the overall decrease in the marine survival between 1971 and 2010 and the sharp decline around 1988–1990 are dampened when density dependence is considered. The return rates of smolts as two-sea-winter (2SW) fish has declined in a higher proportion than return rates as one-sea-winter (1SW) fish. Our results indicate that this can be explained either by an increase in the proportion maturing as 1SW fish or by an increase in the mortality rate at sea of 2SW fish, but the data used in our analyses do not allow the likelihood of these two hypotheses to be gauged