L’évaluation et la gestion des stocks de poissons ont pour objectif d’atteindre une exploitation durable des ressources fournies par les océans. Si les progrès dans ce domaine sont bien réels pour certains stocks de grande importance commerciale, la situation est différente pour les stocks dits à données limitées. Souvent historiquement moins exploités, ces stocks ne bénéficient pas des mêmes ressources, tant économiques qu’humaines, pour réaliser une évaluation de stock permettant par la suite la mise en place de mesures de gestion. Ce travail s’appuie sur deux cas d’étude, le lieu jaune (Pollachius pollachius) et la seiche (Sepia officinalis), afin d’explorer des méthodologies d’évaluation de stocks adaptées aux situations de données limitées. Après une première partie introductive reprenant le contexte de l’évaluation des stocks et présentant les deux cas d’étude, une revue des méthodes d’évaluation de stocks à données limitées est proposée. Une troisième partie compare les résultats d’un modèle de biomasse à deux stades et d’un modèle multi-annuel de déplétion généralisé appliqués au stock de seiche de Manche. Une version améliorée du modèle de biomasse à deux stades codé en Bayésien est également présentée. Le travail se poursuit avec l’application d’un modèle d’analyse intégrée Stock Synthesis au stock de lieu jaune de mer Celtique. Les résultats sont comparés aux résultats de modèles plus simples nécessitant moins de données. Les résultats du modèle Stock Synthesis s’avèrent sensibles aux hypothèses sur la valeur de mortalité naturelle, dont le calcul dépend des paramètres de croissance du stock. La cinquième partie présente l’acquisition et le traitement de nouvelles données qui pourront permettre une meilleure estimation de l’état du stock de lieu jaune. Un modèle hiérarchique Bayésien est construit, permettant un transfert d’information entre trois stocks et la mise à jour des paramètres biologiques du lieu jaune. Le dernier chapitre conclut ce travail en reprenant les principaux résultats obtenus et en élargissant la discussion sur des perspectives de recherche. / The assessment and the management of fish stocks aim at achieving a sustainable exploitation of the resources provided by the oceans. While progress have been made in this field for some stocks of great commercial importance, the situation is different for the so-called “data limited” stocks. Often historically less exploited, these stocks do not benefit from the same economical resources nor workforce to conduct the stock assessments required to set management measures. This work is based on two case studies, pollack (Pollachius pollachius) and cuttlefish (Sepia officinalis). The aim is to investigate the stock assessment methods adapted to data-limited situations. A first introductive part presents the background of fish stock assessment as well as the two case studies. This first chapter is followed by a review of data-limited stock assessment methods. The third part compare the results of a two-stage biomass model with the results of a multi-annual generalized depletion model applied to the English Channel stock of cuttlefish. An improved version of the Bayesian two-stage biomass model is also presented. In the fourth part, a Stock Synthesis model based on integrated analysis methods is applied to the stock of pollack in the Celtic Seas Ecoregion. The results are compared to the results of simpler models which require less data. The Stock Synthesis model results are sensitive to the assumptions on the natural mortality value, which relies on the growth parameters of the stock. The fifth part presents the collection and analysis of new data which will allow a better estimate of pollack stock status. A Bayesian hierarchical model is constructed, allowing information transfer between three stocks and the update of pollack biological parameters. The last chapter concludes this work by summarizing the main results. The discussion is extended to the research perspectives.

Presence of coastal aquaculture activities in marine landscapes is growing. However, there is insufficient knowledge on the subsequent ecological interactions between these activities and marine fish communities. The overall aim of this thesis was to evaluate the direct and indirect ecological effects of aquaculture activities on marine fish communities in Scotland. A combination of empirical and modelling approaches was employed to collect evidence of how aquaculture activities affect marine fish communities at the individual, population and ecosystem levels around coastal sea cages. The two fish farms evaluated in this research provided the wild fish sampled near the sea cages with a habitat rich in food resources which is reflected in an overall better biological condition. Results of the stomach content analysis indicated that mackerel (Scomber scombrus), whiting (Merlangius merlangus) and saithe (Pollachius virens) sampled near sea cages consumed wasted feed which was also reflected in their modified FA profiles. The overall effects of the two fish farms were more pronounced in young whiting and saithe than in mixed aged mackerel sampled near the sea cages. The phase space modelling approach indicated that the overall potential for fish farms to act at the extremes as either population sources (a habitat that is rich in resources and leads to an overall improved fitness) or ecological traps (a habitat that appears to be rich in resources but is not and leads to an overall poor fitness) are higher for juvenile whiting than for mackerel. Based on the empirical evidence and literature the two fish farms are more likely to be a population source for wild fishes. Using an ecosystem modelling approach indicated that fish farming impacts the food web in a sea loch via nutrient loading. Mussel farming relies on the natural food resources and has the potential to affect the food web in a sea loch via competing with zooplankton for resources which can affect higher trophic levels. The presence of both activities can balance the overall impact in a sea loch as compared to the impact induced if each of these activities were present on their own. Both activities have the potential do induce direct and indirect effects on the wild fish and the entire sea loch system. The results of this PhD identified several gaps in data and thus could be used to improve future sampling designs. It is important to evaluate the cumulative effect of the presence of aquaculture activities in terms of nutrient loading and physical structure in the environment. Using a combination of empirical and modelling approaches is recommended to gain further insight into the ecological impacts of aquaculture activities on wild fish communities. Results of this PhD study could lead to more informed decisions in managing the coastal aquaculture activities. Establishing coastal fish farms as aquatic sanctuaries can be of an advantage to increase fish production and conserve species that are endangered provided that no commercial and recreational fishing is allowed nearby. It would be useful to have long term monitoring of the fish stocks around the cages and if there is any production at the regional level. Additionally, information on behaviour, migration patterns should be collected to understand the impacts of aquaculture activities on fish stocks. From an aquaculture perspective, ecologically engineered fish farms in addition to careful site selection in new aquaculture developments may improve nutrient loading into the ecosystem.