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Integrated stock mixture analysis for continous and categorical data, with application to genetic–otolith combinations

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Fish populations or stocks often intermix on fishing grounds, thus posing problems for stock assessors or managers attempting to optimize yields and minimize overexploitation of individual stocks. A Bayesian framework is developed here to simultaneously analyse many of the different data types (e.g., otolith elemental composition, nuclear and mitochondrial DNA) that have been used to identify stock origins of fish in mixed groups and thus take maximal advantage of the available information. Elements of this framework include the capability to analyse each data type either separately or in combination for any number of mixed-group samples, Bayesian credible intervals to evaluate the uncertainty associated with the estimated proportion of the original stocks in the mixed groups, and posterior predictive diagnostics to evaluate the assumptions of the underlying models. The framework was used to re-analyse a subset of otolith elemental composition and microsatellite allele frequency data obtained from the same fish from Atlantic cod (Gadus morhua) stocks in the Gulf of St. Lawrence, Canada.

Les populations ou les stocks de poissons se mélangent souvent sur les aires de pêche, ce qui présente des problèmes pour les évaluateurs de stocks et les gestionnaires qui essaient d’optimiser les rendements et minimiser la surexploitation des stocks individuels. Nous mettons au point ici un cadre bayésien pour analyser simultanément plusieurs des différents types de données (par ex., composition des otolithes en éléments, ADN nucléaire et mitochondrial) qui servent à identifier l’origine des stocks de poissons en peuplements mixtes, pour ainsi tirer un avantage maximal des renseignements disponibles. Ce cadre comporte plusieurs éléments, dont la capacité d’analyser chaque type de données ou bien séparément ou alors en combinaison pour tout nombre d’échantillons de peuplements mixtes, des intervalles bayésiens crédibles pour évaluer l’incertitude associée à la proportion estimée des stocks originaux dans les peuplements mixtes, ainsi que des diagnostics prédictifs a posteriori pour évaluer les présuppositions des modèles sous-jacents. Nous utilisons le cadre pour analyser de nouveau un sous-ensemble de données de compositions des otolithes en éléments et de fréquences alléliques des microsatellites des mêmes poissons provenant de stocks de morues franches (Gadus morhua) du golfe du Saint-Laurent, Canada.

Document Type: Research Article

Publication date: October 1, 2010

More about this publication?
  • Published continuously since 1901 (under various titles), this monthly journal is the primary publishing vehicle for the multidisciplinary field of aquatic sciences. It publishes perspectives (syntheses, critiques, and re-evaluations), discussions (comments and replies), articles, and rapid communications, relating to current research on cells, organisms, populations, ecosystems, or processes that affect aquatic systems. The journal seeks to amplify, modify, question, or redirect accumulated knowledge in the field of fisheries and aquatic science. Occasional supplements are dedicated to single topics or to proceedings of international symposia.
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