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Environmental factors such as water temperature, salinity, and the abundance of zooplankton can have major effects on certain fish stocks' ability to produce juveniles and, thus, stock renewal ability. This variability in stock productivity manifests itself as different productivity regimes. Here, we detect productivity regime shifts by analyzing recruit-per-spawner time series with Bayesian online change point detection algorithm. The algorithm infers the time since the last regime shift (change in mean or variance or both) as well as the parameters of the data-generating process for the current regime sequentially. We demonstrate the algorithm's performance using simulated recruitment data from an individual-based model and further apply the algorithm to stock assessment estimates for four Atlantic cod (Gadus morhua) stocks obtained from RAM legacy database. Our analysis shows that the algorithm performs well when the variability between the regimes is high enough compared with the variability within the regimes. The algorithm found several productivity regimes for all four cod stocks, and the findings suggest that the stocks are currently in low productivity regimes, which have started during the 1990s and 2000s. Des facteurs environnementaux tels que la temperature et la salinite de l'eau et l'abondance du zooplancton peuvent avoir des effets significatifs sur la capacite de certains stocks de poissons a produire des juveniles et, donc, sur la capacite de renouvellement de ces stocks. Cette variabilite de la productivite d'un stock se manifeste sous la forme de differents regimes de productivite. Nous recensons des changements de regime de productivite en analysant des series chronologiques de recrues par geniteur a l'aide d'un algorithme bayesien de detection des points de changement en ligne. L'algorithme infere sequentiellement le temps ecoule depuis le dernier changement de regime (changement de la moyenne ou de la variance ou les deux), ainsi que les parametres du processus de generation de donnees pour le regime actuel. Nous demontrons la performance de l'algorithme en utilisant des donnees de recrutement simulees issues d'un modele base sur l'individu et appliquons egalement l'algorithme a des estimations devaluation des stocks pour quatre stocks de morue (Gadus morhua) obtenues de la base de donnees existantes RAM. Notre analyse montre que l'algorithme performe bien quand la variabilite entre les regimes est suffisamment elevee par rapport a la variabilite au sein des regimes. L'algorithme a decele plusieurs regimes de productivite pour chacun des quatre stocks de morues, et les resultats donnent a penser que ces stocks sont actuellement dans des regimes de faible productivite qui ont debute durant les annees 1990 et 2000. [Traduit par la Redaction], Introduction Marine ecosystems can undergo rapid changes from one relatively stable state to another because of alterations in environmental conditions. These changes from one state to another are often called [...]

The abundance-occupancy relationship is one of the most well-examined relationships in ecology. At the species level, a positive association has been widely documented. However, until recently, research on the nature of this relationship at broad taxonomic and spatial scales has been limited. Here, we perform a comparative analysis of 12 taxonomic groups across a large spatial scale (Canada), using data on Canadian species at risk: amphibians, arthropods, birds, freshwater fishes, lichens, marine fishes, marine mammals, molluscs, mosses, reptiles, terrestrial mammals, and vascular plants. We find a significantly positive relationship in all taxonomic groups with the exception of freshwater fishes (negative association) and lichens (no association). In general, our work underscores the strength and breadth of this apparently fundamental relationship and provides insight into novel applications for large-scale population dynamics. Further development of species-independent abundance-occupancy relationships, or those of a similar nature, might well prove instrumental in serving as starting points for developing species-independent reference points and recovery strategies. Key words: population dynamics, species abundance, recovery targets, conservation strategies, mammals, amphibians. La relation abondance-occupation est une des relations les plus intensement examinees en ecologie. A l'echelle de l'espece, une association positive est abondamment documentee. Jusqu'il tout recemment, cependant, la recherche sur la nature de cette relation a de larges echelles taxonomiques et spatiales etait limitee. Nous realisons une analyse comparative de 12 groupes taxonomiques sur une grande echelle spatiale (le Canada) en utilisant des donnees sur les especes en peril canadiennes, comprenant des amphibiens, arthropodes, oiseaux, poissons d'eau douce, lichens, poissons de mer, mammiferes marins, mollusques, mousses, reptiles, mammiferes terrestres et plantes vasculaires. Nous constatons une relation positive significative dans tous les groupes taxonomiques, a l'exception des poissons d'eau douce (association negative) et des lichens (pas d'association). En general, nos travaux font ressortir la force et l'etendue de cette relation apparemment fondamentale et mettent en lumiere de nouvelles applications pour l'etude de la dynamique des populations a grande echelle. D'autres avancees sur les relations abondance-occupation independantes des especes ou de relations de nature similaire pourraient bien s'averer utiles comme points de depart pour l'etablissement de points de reference et de strategies de retablissement independants des especes. [Traduit par la Redaction] Mots-cles: dynamique des populations, abondance des especes, cibles de retablissement, strategies de conservation, mammiferes, amphibiens., Introduction The relationship between the abundance of a species and its geographical range, more classically termed the abundance-occupancy relationship, is one of the best studied in macroecology (Brown 1984; Blackburn [...]

Recovery targets for threatened species are typically developed on a species- or population-specific basis. Such narrow taxonomic specificity stands in contrast with widely applied species-independent metrics of conservation status. Here, we propose a generic protocol that can be used to specify broadly applicable targets intended to recover the ecological and evolutionary functionality of threatened species. The method is based on basic density-dependent population dynamics, draws on first principles related to population growth, and explicitly incorporates habitat by accounting for changes in carrying capacity. It offers a consistently applied, methodologically transparent, and predictable biological benchmark for recovery purposes. The benefits of a generic method for articulating recovery targets, particularly from a policy- and statute- implementation perspective, are substantive. Key words: carrying capacity, population growth rate, policy implementation, density dependence, reference point. Les cibles de retablissement pour les especes menacees sont typiquement etablies sur la base de l'espece ou de la population. Une specificite taxinomique aussi stricte contraste avec les parametres independants de l'espece largement appliques pour caracteriser la situation des especes en ce qui concerne leur conservation. Nous proposons un protocole generique pouvant etre utilise pour definir des cibles d'application large de retablissement de la fonction ecologique et evolutionnaire d'especes menacees. La methode repose sur la dynamique des populations dependante de la densite, s'appuie sur des principes de base associes a la croissance des populations et integre explicitement l'habitat en tenant compte des variations de la capacite de charge. Elle fournit un test de performance biologique previsible, d'application uniforme, et transparent sur le plan methodologique pouvant etre utilise a des fins de retablissement. Les avantages d'une methode generique pour definir des cibles de retablissement, particulierement dans une perspective d'application des politiques et lois, sont considerables. [Traduit par la Redaction] Mots-cles : capacite de charge, taux de croissance de la population, application des politiques, dependance de la densite, point de reference., Introduction The assessment of conservation status (e.g., 'endangered', 'threatened') by many national and international bodies is based on broad, species-independent criteria intended to reflect extinction probability, developed by the International [...]

Excessively high rates of fishing mortality have led to rapid declines of several commercially important fish stocks. To harvest fish stocks sustainably, fisheries management requires accurate information about population dynamics, but the generation of this information, known as fisheries stock assessment, traditionally relies on conservative and rather narrowly data-driven modelling approaches. To improve the information available for fisheries management, there is a demand to increase the biological realism of stock-assessment practices and to better incorporate the available biological knowledge and theory. Here, we explore the development of fisheries stock- assessment models with an aim to increasing their biological realism, and focus particular attention on the possibilities provided by the hierarchical Bayesian modelling framework and ways to develop this approach as a means of efficiently incorporating different sources of information to construct more biologically realistic stock-assessment models. The main message emerging from our review is that to be able to efficiently improve the biological realism of stock-assessment models, fisheries scientists must go beyond the traditional stock-assessment data and explore the resources available in other fields of biological research, such as ecology, life-history theory and evolutionary biology, in addition to utilizing data available from other stocks of the same or comparable species. The hierarchical Bayesian framework provides a way of formally integrating these sources of knowledge into the stock-assessment protocol and to accumulate information from multiple sources and over time. Key words: Bayesian statistics, fisheries management, harvesting, life histories, overfishing, stock assessment. Des taux de mortalite excessifs de poissons ont conduit a des declins rapides de plusieurs stocks de poissons commerciaux importants. Afin de recolter de facon durable les stocks de poissons, l'amenagement des pecheries necessite une information precise sur la dynamique des populations, mais la generation de cette information, connue sous le nom d'evaluation des stocks de poissons, repose traditionnellement sur la conservation plutot qu'a des approches de modelisation conduites a partir de donnees precises. Afin d'ameliorer l'information disponible pour l'amenagement des pecheries, on observe une demande croissante pour l'ameliorer du realisme biologique des pratiques d'evaluation des stocks et pour mieux incorporer la connaissance et la theorie biologique disponibles. Les auteurs examinent le developpement de modeles d' evaluation des stocks de poissons avec l'objectif d'augmenter leur realisme biologique, et de porter une attention particuliere sur les possibilites provenant du cadre de modelisation bayesien ainsi que les facons de developper cette approche comme moyen d'incorporer efficacement differentes sources d' information permettant de construire des modeles plus realistes pour l' evaluation des stocks. Le principal message emergeant de cette revue est a l'effet que pour arriver a ameliorer efficacement le realisme des modeles d'evaluation des stocks, les specialistes des pecheries doivent aller au-dela des donnees traditionnelles d' evaluation des stocks et explorer les ressources disponibles dans d'autres champs de recherche biologique, comme l'ecologie, la theorie du cycle vital et la biologie evolutive, en plus d' utiliser les donnees disponibles a partir d'autres stocks de la meme ou d' especes comparables. Le cadre bayesien hierarchique fournit une facon d'integrer formellement ces sources de connaissances dans le protocole d'evaluation des stocks et d' accumuler de l' information a partir d'autres sources avec le temps. Mots-cles : statistiques bayesiennes, amenagement des pecheries, recolte, cycle vital, surpeche. [Traduit par la Redaction], Introduction Numerous commercially exploited fish stocks have rapidly declined as a result of excessively high rates of fishing mortality (FAO 2010). The demographic consequences of overexploitation have been realised through [...]

Many considerably declined fish populations have not fully recovered despite reductions in fishing pressure. One of the possible causes of impaired recovery is the (demographic) Allee effect. To investigate whether low‐abundance recruitment dynamics can switch between compensation and depensation, the latter implying the presence of the Allee effect, we analysed the stock–recruitment time series of 17 depleted cod‐type and flatfish populations using a Bayesian change point model. The recruitment dynamics were represented with the sigmoidal Beverton–Holt and the Saila–Lorda stock–recruitment models, allowing the parameters of the models to shift at a priori unknown change points. Our synthesis study questions the common assumption that recruitment is stationary and compensatory and the high amount of scatteredness often present in stock–recruitment data is only due to random variation. When a moderate amount of such variation was assumed, stock–recruitment dynamics were best explained by a non‐stationary model for 53% of the populations, which suggests that these populations exhibit temporal changes in the stock–recruitment relationship. For four populations, we found shifts between compensation and depensation, suggesting the presence of temporary Allee effects. However, the evidence of Allee effects was highly dependent on the priors of the stock–recruitment model parameters and the amount of random variation assumed. Nonetheless, detection of changes in low‐abundance recruitment is essential in stock assessment since such changes affect the renewal ability of the population and, ultimately, its sustainable harvest limits. [ABSTRACT FROM AUTHOR]