The growth rate of a fish is a fundamental function used in stock assessments to estimate the population size and the fishery pressure affecting the species. There has been recent debate within the stock assessment community regarding which type of growth model best represents the true growth rate of yellowfin tuna (Thunnus albacares), in the Atlantic Ocean; specifically, should assessments use a traditional von Bertalanffy growth curve or a so-called “two-stanza” growth curve, which combines one growth rate for smaller individual tuna and another for larger sizes. Using a simulated population created with the software R, both growth models were compared under different scenarios. The first part of this thesis examines the effect of different fisheries and their associated gear selectivity. Purse seine, baitboat and pelagic longline fisheries, which target yellowfin tuna in the Atlantic Ocean, were incorporated into the analysis. The second part looks at different sources of variability that occur either in nature (observation error) or in the process of analysis (process error). These include different growth variation, looking only at the fast growing young fish and using a set birth date versus a spawning period. These scenarios were used to determine if the sample, derived from a fishery-dependent sample, reflects the true population. Three populations of yellowfin tuna were created: an un-fished population, a fished population from stock assessment data, and a fished population from simulation software called ‘Population Simulator’. These populations were all analyzed for the different scenarios as well as the different fisheries. The final part of this thesis looks at three similar tuna species; skipjack (Katsuwonus pelamis), bigeye (Thunnus obesus ) and albacore (Thunnus alalunga). The same scenarios and gear selectivities were applied to these tuna species. The results of this study showed that the two-stanza growth curve was not a better fit for yellowfin tuna population in the Atlantic Ocean than the traditional von Bertalanffy growth curve. There were several scenarios that favored the two-stanza growth curve, but either it was a sample population not representative of the Atlantic Ocean population, or the two-stanza had no initial growth rate, making it the same as a traditional growth curve. Based on these results, it was evident that the traditional von Bertalanffy growth curve was the more accurate growth curve to use for yellowfin tuna in the Atlantic Ocean and it is recommended that this growth curve be used in the stock assessments going forward.

La modélisation de la dynamique des populations de thons et grands pélagiques pour l'évaluation des stocks est confrontée à deux enjeux majeurs. (1) L'hypothèse forte de proportionnalité entre Captures Par Unité d'Effort de pêche (CPUE) et l'abondance des stocks. Les CPUE des pêcheries commerciales sont en effet les seules mesures relatives de biomasse utilisées pour l'évaluations des stocks de thons et grands pélagiques, malgré leur manque de représentativité de l'abondance de ces populations. (2) Le manque de données informatives pour modéliser la relation Stock-Recrutement (SR) ce qui conduit à utiliser des contraintes sur la "steepness" de cette fonction. Nous examinons comment l'introduction d'informations indépendantes des pêcheries commerciales dans les modèles pour l'évaluation des stocks thoniers permet de lever l'hypothèse de capturabilité constante et de mieux justifier le choix de la steepness de la relation SR. Le cadre statistique bayésien autorise la prise en compte d'informations supplémentaires via des distributions a priori informatives (priors). Cette thèse examine donc les possibilités d'élicitation de priors informatifs pour des paramètres démographiques et des paramètres liés à la capturabilité des engins de pêche, ainsi que l'utilisation de ces priors dans un modèle global. Les cas d'études sont les stocks de thon rouge (Thunnus thynnus) et d'albacore (Thunnus albacares) de l'Atlantique. La grande variabilité naturelle des taux de mortalités pré-recrutement pose des limites à l'utilisation des seuls traits d'histoire de vie pour l'élicitation de priors pour des paramètres démographiques. Par ailleurs, la relation SR pour les thonidés est remise en question par une valeur de steepness proche de 1. Il apparait que des priors informatifs sur la capturabilité dans un modèle hiérarchique global permettent de réduire les incertitudes dans le diagnostic sur l'état d'un stock thonier. Nous montrons ainsi que le diagnostic sur le stock Atlantique d'albacore est plus pessimiste qu'attendu la tendance à la hausse des capturabilités des principaux engins de pêche est prise en compte. L'élicitation de priors présente donc un fort intérêt pour utiliser des informations supplémentaires et extérieures aux CPUE et améliorer la perception de l'état des stock thoniers. / Modelisation of the population dynamics of tunas and tuna like species for stock assessment is facing two issues. (1) The hypothesis of proportionality between Catch Per Unit Effort (CPUE) and abundance (constant catchability). CPUEs from commercial fisheries appear to be the only relative measure of abundance in spite of their lack of representativity of the abundances of the populations. (2) The lack of informative data for the modelisation of the Stock-Recruit (SR) relationship, which leads to constraint this function on its steepness. The introduction of fisheries-independent sources of information is investigated in order to relax the assumption of constant catchability and to provide better justification of steepness choice for the SR relationship. The Bayesian statistical framework allows the consideration of additional information a priori via informative distributions (priors). This work investigate the elicitation of informative priors for demographic parameters and parameters related to the catchability of fishing gear, as well as the use of these priors into a surplus production model. The cases of the Atlantic bluefin tuna (Thunnus thynnus) and of the yellowfin tuna (Thunnus albacares}) were taken as examples. The large natural variability of pre-recruits mortality rates limits the use of life history traits for eliciting priors for demographic parameters. In addition, the SR relationship for tuna is challenged by a steepness value close to 1. It appears that informative priors on catchability parameters, in a hierarchical surplus production model, reduce uncertainties in the diagnosis on the status of tuna stocks. We show that the status of the Atlantic yellowfin tuna stock is more critical taking into account upward trends in the main fishing gears catchabilities. We conclude that prior elicitation is a reliable tool to take into account additionnal information and to improve tunas stock assessment.

This study examined the effects of the January 2010 cold spell on mangrove utilizing coral reef fishes off the southeast coast of Florida, USA, in the vicinity of Biscayne National Park (BNP). An ongoing, fishery-independent mangrove visual survey documenting fish assemblages in BNP provided data from the years 1998 to 2014 for examination. Of particular interest were the presence, abundance, and size structure for five mangrove utilizing coral reef fishes: sergeant major (Abudefduf saxatilis), yellowfin mojarra (Gerres cinereus), schoolmaster snapper (Lutjanus apodus), gray snapper (Lutjanus griseus), and great barracuda (Sphyraena barracuda). These species were selected for analysis due to their economic and ecologic importance, their potential as environmental indicators, their connectedness to multiple habitats, and their abundance within the available data set. Data were collected using a modified visual ‘belt transect’ method, consisting of 60 m2 transects running parallel to the mangrove shorelines. Data for average length of fish were reconstructed to form standard normal distributions and the resulting lengths were assigned to various age-classes to create species-specific length-frequency distributions. Variations in presence and abundance were examined across three time periods (1998-2009; 2010-2011; 2012-2014), as well as comparisons of length-frequency distributions. Following the January 2010 cold spell, the presence and abundance values for the two years immediately following the event were significantly decreased compared to the years prior to the cold spell for most of the five species at either mainland (ML) or leeward key (LK) locations. Additionally, the presence and abundance estimates typically remained statistically decreased when compared against the remaining years in the available data set. The size structures for the majority of the five species at either location, however, were not consistently significantly different between the three time periods, as was hypothesized. Instead, the analyses showed mixed results, with the size structure typically shifting towards smaller individuals immediately following the event. These findings suggest that drops in water temperature resulting from cold spells are capable of directly impacting mangrove utilizing reef fish species, albeit to varying degrees depending on various factors, such as physiological tolerances, ecological life history strategies, and habitat requirements.

Le thon obèse (Thunnus obesus), le thon alabore (Thunnus albacares) et le listao (Katsuwonus pelamis) comptent parmi les espèces de thons les plus utilisées en conserve. Lors de la fabrication de conserves de thon, la substitution d'espèce et/ou le mélange de différentes espèces de thon sont interdits par la réglementation européenne. L'authentification des espèces de thon reste complexe à cause du degré de similitude élevé entre les espèces de thon, ou encore, lorsque les caractéristiques morphologiques externes sont éliminées au cours du filetage et lors de la mise en conserve. Par conséquent, des substitutions involontaires ou frauduleuses peuvent se produire. Dans cette étude, le marqueur mitochondrial du gène de la sous-unité 2 de la NADH déshydrogénase a été utilisé pour identifier le thon obèse et le gène de la sous-unité II de la cytochrome c oxydase a été utilisé pour identifier le thon albacore et le listao en utilisant la PCR en temps réel basée sur la technologie TaqMan. Deux méthodes différentes basées sur la qPCR ont été développées pour quantifier le pourcentage de chair de chaque espèce présente au sein d'une boîte de thon. La première a été basée sur la quantification absolue avec standard externe réalisée avec les deux marqueurs. La seconde a été basée sur la quantification relative avec standard externe avec le gène endogène de l'ARN 12S. Sur la base de ces résultats, nous pouvons conclure que notre méthode peut s'appliquer pour quantifier les deux espèces de thon albacore et obèse génétiquement très proches lorsqu'elles sont utilisées dans un mélange binaire en conserve. / Bigeye tuna (Thunnus obesus), yellowfin tuna (Thunnus albacares) and skipjack tuna (Katsuwonus pelanis) are among the most widely used tuna species for canning purposes. Not only substitution but also mixing of tuna species is prohibited by the European regulation for canned tuna products. However, it can be difficult to authenticate the tuna species, due to their high degree of similarity or even when the external morphological characteristics are removed due to filleting before canning. Consequently, involuntary or fraudulent substitutions may occur during the canning process. In this study, the mitochondrial marker from NADH dehydrogenase subunit 2 gene was used to identify bigeye tuna and the mitochondrial marker cytochrome c oxidase subunit II gene was used to identify yellowfin tuna and skipjack tuna, utilizing TaqMan qPCR methodology. Two different qPCR-based methods were developed to quantify the percentage of flesh of each species used for can processing. The first one was based on absolute quantification using standard curves realized with these two markers ; the second one was founded on relative quantification with the universal 12S rRNA gene as the endogenous gene. On the basis of our results, we conclude that our methodology could be applied to authenticate the two closely related tuna species (bigeye tuna and yellowfin tuna) when used in a binary mix in tuna cans.