Le déclin du thon rouge de l'Atlantique nord-est et de Méditerranée (ABFT, Thunnus thynnus) qui faisait suite à une forte surexploitation a été largement médiatisé au cours de la dernière décennie. Pour contrer cette tendance et reconstituer ce stock, d’importantes mesures de gestion ont été mises en place à partir de 2007. En dehors des difficultés liées à leur mise en œuvre et à leur contrôle, la gestion des pêcheries thonières est aussi limitée dans les capacités à suivre précisément les variations d’abondance de ces espèces dont les observations reposent principalement sur les données de pêche. Le manque d’indice d’abondance fiable fait que l’évaluation du thon rouge, comme celle des autres espèces de poissons grands pélagiques, est entachée d’importantes incertitudes. Cependant, les suivis aériens pourraient permettre de fournir un indice d’abondance du thon rouge. Ils sont en effet fréquemment utilisés pour l'évaluation de l'abondance des mammifères marins et aussi par les pêcheurs pour détecter les poissons épipélagiques, comme les thons. Dans ce contexte général, cette thèse a pour objectifs : (i) d'évaluer des facteurs qui affectent potentiellement la détectabilité des thons pendant les suivis aériens, (ii) d’analyser leur comportement horizontal et vertical et les facteurs environnementaux qui l’influencent, et (iii) d’intégrer les connaissances acquises pour développer un indice abondance robuste du thon rouge en Méditerranée Nord Occidentale. Les analyses reposent sur des suivis aériens conduits depuis 2000 dans le golfe du Lion, une zone de nourricerie importante pour le thon rouge. Une modélisation des données basée sur le « distance sampling » montre des effets significatifs des observateurs, de la taille des bancs de thons et de l'état de la mer sur l’estimation d’abondance. Cette étude confirme par ailleurs une augmentation importance des abondances entre 2003 et 2009, probablement en réponse aux mesures de gestion mises en œuvre depuis 2007 (notamment la taille minimale de débarquement de 30 kg). Pour évaluer les effets du comportement sur les estimations d'abondance, une étude a porté sur les trajectoires de thons issues du marquage électronique. Ces analyses montrent une disponibilité des thons rouge ainsi qu’une présence en surface dans la zone et la période (Août-Octobre) des suivis aériens ; résultat confortant la fiabilité de l’indice d’abondance. On note également des changements saisonniers du comportement, avec un approfondissement des thons à partir de mi-Novembre correspondant à la dé-stratification de la colonne d’eau. Le comportement de plongée profonde était particulièrement fréquent pendant les mois de forte productivité biologique (février-Mai), mais des plongées profondes ont également été observées à la fin de l'été en relation avec des fronts thermiques. La variabilité des schémas migratoires sur l’horizontale et du comportement sur la verticale indique une forte composante opportuniste, probablement liée à la disponibilité des ressources alimentaires. Les résultats obtenus durant cette thèse démontrent la faisabilité d’obtenir un indice d’abondance de thon rouge robuste à partir des suivis aériens (donc indépendants des données de pêche) et fournissent un cadre théorique et méthodologique pour une extension de ce type de suivi afin de diminuer les incertitudes autour de l’évaluation de ce stock. Outre le thon rouge, les suivis aériens ont également permis un suivi du rorqual commun (Balaenoptera physalus) et des dauphins rayés (Stenella coeruleoalba). La présence des mammifères marins semble également être liée à la productivité élevée et l'activité méso-échelle de la zone d'étude. Si les dauphins présentent une distribution spatiale en partie corrélée à celle du thon rouge, les rorquals ne présentent pas de forte co-occurrence avec le thon rouge, résultat qui confirmerait une certaine proximité des régimes alimentaires des thons et des dauphins. / Declines in Atlantic bluefin tuna stocks (ABFT, Thunnus thynnus), due to extensive over-fishing, have been widely publicized in recent decades. To counteract this trend, regulatory measures have been introduced by the fisheries managers, aiming at the rebuilding of ABFT stocks. However, apart from difficulties in controlling the implementation of these measures, fisheries management is limited in its capabilities to track their efficiency due to major uncertainties in the stock assessment. Indeed, there is a general need of reliable indicators of ABFT abundance. Aerial surveys may provide a helpful tool for the abundance monitoring of this highly exploited fish species. They are frequently used for the abundance assessment of marine mammals and also by fishermen to detect epipelagic fish, such as tunas. The aim of this thesis was to address these issues and to create a robust fishery-independent abundance index for ABFT through aerial surveys. To achieve this goal, the focus was set on (i) the assessment of factors that potentially affect the detectability of ABFT during the aerial surveys, (ii) the habitat use of ABFT, i.e. their horizontal and vertical behaviour as well as the factors driving it, and (iii) the integration of the knowledge gained through these analyses in the development of a robust index of ABFT abundance. Surveys were conducted from 2000 onwards in the Gulf of Lions, an important nursery ground for ABFT in the Northwestern Mediterranean Sea. Line transect modelling of the sighting data revealed significant effects of detectability changes on abundance estimates, related to the observer teams employed, the size of detected ABFT schools and the sea state during the aerial surveys. Derived estimates of ABFT abundance confirmed a significant increase from 2003 to 2009, likely reflecting the success of recently implemented management measures (e.g. minimum landing size of 30 kg since 2007). To assess behavioural effects on abundance estimates, auxiliary archival tagging experiments, conducted since 2007, focused on the presence and surface availability of ABFT during the aerial surveys, and aimed to identify factors influencing these variables. The data gained from these experiments demonstrated seasonal changes in the migratory behaviour of ABFT, but also a high area and surface presence of ABFT in the study zone during the survey period (August–October), supporting the reliability of the abundance index. Surface presence of ABFT decreased with the breakdown of the thermal stratification of the water column (mid-November), when the fish left the survey zone and moved South. By contrast, deep diving behaviour was particularly frequent during months of high biological productivity (February--May), although deep and unusual long spike dives were also observed during late summer in relation to thermal fronts. However, the variability in the migration patterns indicates a strong opportunistic component in both, the horizontal and vertical behaviour of ABFT, probably related to the availability of food resources. Apart from ABFT, the aerial surveys also allowed an abundance monitoring of fin whales (Balaenoptera physalus) and striped dolphins (Stenella coeruleoalba) as well as an analysis of their co-occurrence with ABFT. In fact, similar to ABFT, the presence of these species appeared to be related to the high productivity and mesoscale activity of the study zone, improving our understanding of their habitat use, essential for the conservation of these much less abundant and endangered species. Regarding the stock assessment of ABFT, the results gained through this thesis prove the feasibility to derive robust fishery independent abundance indicators for ABFT through aerial surveys, providing the theoretical and methodological background for an extension of these efforts for a more sustainable management of the stocks of this species.

Yellow perch (Perca flavescens) in Lake Erie support valuable commercial and recreational fisheries critical to the local economy and society. The study of yellow perch's temporal and spatial population dynamics is important for both stock assessment and fisheries management. I explore the spatial and temporal variation of the yellow perch population by analyzing the fishery-independent surveys in Lake Erie. Model-based approaches were developed to estimate the relative abundance index, which reflected the temporal variation of the population. I also used design-based approaches to deal with the situation in which population density varied both spatially and temporally. I first used model-based approaches to explore the spatial and temporal variation of the yellow perch population and to develop the relative abundance index needed. Generalized linear models (GLM), spatial generalized linear models (s-GLM), and generalized additive models (GAM) were compared by examining the goodness-of-fit, reduction of spatial autocorrelation, and prediction errors from cross-validation. The relationship between yellow perch density distribution and spatial and environmental factors was also studied. I found that GAM showed the best goodness-of-fit shown as AIC and lowest prediction errors but s-GLM resulted in the best reduction of spatial autocorrelation. Both performed better than GLM for yellow perch relative abundance index estimation. I then applied design-based approaches to study the spatial and temporal population dynamics of yellow perch through both practical data analysis and simulation. The currently used approach in Lake Erie is stratified random sampling (StRS). Traditional sampling designs (simple random sampling (SRS) and StRS) and adaptive sampling designs (adaptive two-phase sampling (ATS), adaptive cluster sampling (ACS), and adaptive two-stage sequential sampling (ATSS)) for fishery-independent surveys were compared. From accuracy and precision aspect, ATS performed better than the SRS, StRS, ACS and ATSS for yellow perch fishery-independent survey data in Lake Erie. Model-based approaches were further studied by including geostatistical models. The performance of the GLM and GAM models and geostatistical models (spatial interpolation) were compared when they are used to analyze the temporal and spatial variation of the yellow perch population through a simulation study. This is the first time that these two types of model- based approaches have been compared in fisheries. I found that arithmetic mean (AM) method was only preferred when neither environment factors nor spatial information of sampling locations were available. If the survey can not cover the distribution area of the population due to biased design or lack of sampling locations, GLMs and GAMs are preferable to spatial interpolation (SI). Otherwise, SI is a good alternative model to estimate relative abundance index. SI has rarely been realized in fisheries. Different models may be recommended for different species/fisheries when we estimate their spatial-temporal dynamics, and also the most appropriate survey designs may be different for different species. However, the criteria and approaches for the comparison of both model-based and design-based approaches will be applied for different species or fisheries. / Ph. D.