La daurade royale (Sparus aurata, L.) est une espèce migratrice, connue pour coloniser les lagunes côtières, fortement anthropisées, du printemps à l'automne. Identifier les lagunes clés pour l'accomplissement du cycle de vie doit donc permettre de mieux gérer et protéger les populations de daurades du Golfe du Lion. Dans ce cadre, la microchimie de l'otolithe est un outil précieux. Au cours de sa croissance, cette concrétion de l'oreille interne incorpore des éléments chimiques prélevés dans le milieu. Piégés dans le réseau cristallin, ils sont une image des conditions environnementales rencontrées par le poisson à une date donnée ce qui rend possible, en théorie, de reconstituer ses migrations. Néanmoins, pour cela, il faut (i) connaître précisément la croissance du poisson et de ses otolithes, (ii) mettre en évidence des différences chimiques entre les zones clés pour le cycle de vie en identifiant les outils statistiques appropriés pour la discrimination des habitats. Ainsi, (i) la comparaison objective de modèles de croissance, associée à l'analyse d'un spécimen exceptionnellement âgé a permis de remettre en cause les données classiquement acceptées sur la croissance de la daurade et le schéma de croissance de ses otolithes a été établi ; (ii) la comparaison de 4 méthodes statistiques de discrimination a permis de sélectionner la méthode du random forest pour différencier les signatures chimiques des otolithes de S.aurata de différentes lagunes. Ces avancées ont permis de confirmer le schéma migratoire précédemment décrit, tout en révélant une variabilité des comportements entre les individus et au cours de la vie du poisson. Les juvéniles semblent préférer les lagunes dessalées, suggérant un rôle de nurserie pour ces habitats, alors que les adultes préfèrent des lagunes profondes comme l'étang de Thau. Le maintien de la diversité des caractéristiques des différentes lagunes est donc nécessaire, afin d'assurer la pérennité de la population de S.aurata dans le Golfe du Lion. / The Gilthead seabream (Sparus aurata L.) is a migratory species, known to colonize coastal lagoons with high anthropogenic load, from spring to autumn. It is necessary to identify key lagoons for the seabream life cycle to allow better management and protection of gilthead seabream populations in the Gulf of Lions. For this, otolith microchemistry is a powerful tool. As it grows, this inner ear concretion absorbs chemical elements taken in its surrounding. Traped in the crystal net, these elements are an image of the environmental conditions met by the fish individual. It is then possible to rebuild fish past migrations. For this it is necessary to (i) precisely know the fish and otoliths growth calendars and (ii) identify chemical differences between the key habitats for the life cycle by choosing statistical methods for habitat discrimination.(i) The objective comparison of many growth models, combined to the analysis of an exceptionally old specimen allowed to propose a new scheme for the gilthead seabream growth and its otolith growth pattern was established ; (ii) the comparison of 4 statistical discrimination methods allowed to select the random forest method to differentiate the otolith chemical signatures of gilthead seabreams from various lagoons. These insights confirmed the already described migration pattern and emphasized a behavioural variability between individuals and between periods of life. The juveniles seem to prefer brackish lagoons, suggesting a nursery rôle for these habitats, whereas the adults prefer deeper lagoons as the Thau lagoon. The maintenance of the lagoons diversity is thus necessary for the preservation of the Gilthead seabream population in the Gulf of Lions.

La sole commune présente au cours de son cycle de vie un changement ontogénétique d’habitat. Les larves sont marines et pélagiques, les juvéniles sont benthiques et vivent dans les nourriceries côtières (lagunes et estuaires) alors que les adultes sont benthiques et marins en zones plus profondes. Les otolithes sont des concrétions minéralisées de carbonate de calcium de l’oreille interne des téléostéens qui ne subissent ni dissolution ni résorption. Ils enregistrent les caractéristiques chimiques et isotopiques des milieux traversés.L’étude de la croissance, de la composition chimique et isotopique des otolithes des soles des nourriceries a confirmé l’existence de deux stocks de soles dans le golfe du Lion, un à l’Est et l’autre à l’Ouest. Les faibles valeurs de 13C et les fortes valeurs de Ba/Ca des otolithes des soles de l’Est du golfe ont été associées à une forte influence des apports rhodaniens sur la phase de vie larvaire lors des années où le débit du Rhône est normal. En période de crue, une forte influence du fleuve est visible sur les otolithes des soles des nourriceries de l’ensemble du golfe. La croissance des otolithes des juvéniles a été plus élevée lorsque la salinité a été proche de 20 et la température comprise entre 20 et 25°C (période estivale). Les signatures des otolithes de Mauguio et Berre ont présenté des 13C et Sr/Ca plus faibles que ceux de Thau (influences plus marines sur les proies et les masses d’eau). La spécificité des signatures chimiques et isotopiques des otolithes a permis d’élaborer des profils qui ont été retrouvés chez les populations de soles adultes du golfe, mais aussi vers Marseille et Bandol. Ces soles ont montré une influence du Rhône durant la phase de vie larvaire à 53%. Elles ont également montré une forte similarité avec les profils chimiques de type lagune de Thau (10-56%) et Rhône (19-30%) durant leur vie juvénile. Toutefois, une proportion non négligeable de soles originaires de nourriceries non caractérisées (26-50%) a été observée. / The life cycle of the common sole shows an ontogenetic shift of habitats. The larvae are marine and pelagic, the juveniles are benthic in coastal nurseries (lagoons and estuaries) whereas adults are benthic and live in marine deeper areas. Otoliths are paired calcified structures from the inner ear of teletost fish. They are metabolically inert (neither resorption nor dissolution) and they record, both the age (daily and annual increments) and the chemical and isotopic characteristics of the environment inhabited. Otoliths study provides information on the life history traits of individuals.The study of growth, chemical and isotopic otolith composition of soles from nurseries confirmed the existence of two sole stocks in the Gulf of Lions, one in the Eastern part and the other in the Western part. Low values in 13C and higher values in Ba/Ca ratio measured in Eastern sole otoliths during the larval life were associated to a high influence of the Rhône River discharge during a normal flow rate periods. Conversely, the one hundred return flood of the 2nd of December 2003 was very high and visible on otoliths from all nurseries in the Gulf of Lions. Juvenile otolith growth was higher in nurseries with low salinity (~20) and temperatures between 20 and 25°C than in more marine nurseries. 13C and Sr/Ca ratios of otoliths from Berre and Mauguio coastal lagoons were lower than those observed in Thau coastal lagoon (more marine influences on preys and water masses). These specificities of otolith compositions were used for the elaboration of reference profiles, which have been identified in adult populations of the Gulf of Lions, Marseilles and Bandol. Adult have shown an influence of the Rhône River during their larval life at 53%. They have shown a similarity with Thau chemical profile (10-56%) and Rhône profile (19-30%) during their juvenile life. However, 26-50% of fish from uncharacterised nurseries have been observed.

La daurade royale (Sparus aurata) est une espèce de sparidé dont l’aire de répartition s’étend des côtes du Sénégal à l’Irlande, et est commune en mer Méditerranée. Elle est considérée comme rare en limite nord de répartition (Manche, mer d’Irlande et mer du Nord). Depuis une dizaine d’années, l’abondance d’individus pêchés en limite nord ne cesse d’augmenter. Ce phénomène peut être expliqué par l’évolution septentrionale de son aire de répartition, en lien avec le réchauffement climatique. Aucune donnée écologique sur les populations de cette espèce en limite nord de répartition, devenues une ressource de pêche en Manche, n’est actuellement publiée dans la littérature. Les traits de vie de S. aurata ont été étudiés face à la modification spatio-temporelle de son aire de répartition, via l’analyse du régime alimentaire, de la croissance et des déplacements côtiers. D’autre part, l’étude a conduit à l’analyse de la structure de ces populations septentrionales par une approche multi-marqueur couplant la génétique et la microchimie des otolithes.L’analyse des contenus stomacaux des populations de S. aurata en limite nord de répartition confirme un régime opportuniste, avec une forte proportion d’espèces-proies du genre Mytilus. Malgré un régime alimentaire similaire, la croissance des individus est, quant à elle, plus faible que celle observée sur des individus de mer Méditerranée, ce phénomène étant conditionné par les paramètres du milieu (température, salinité). Les variations élémentaires des otolithes ont permis de caractériser les migrations côtières lors des premières années de vie des poissons avec un passage en mer en hiver et la fréquentation de zones côtières. Cela suggère la présence de zones de nourricerie le long du pourtour atlantique et de la Manche. Une variabilité inter-individuelle a été mise en évidence suggérant une plasticité comportementale des individus. Les approches de génétique, combinant l’emploi de marqueurs mitochondriaux et des microsatellites, et de microchimie des otolithes ont mis en évidence l’absence de structure au sein des populations en limite nord de répartition. Ce phénomène concorde avec la colonisation récente des populations. Cependant, une différenciation entre les individus échantillonnés le plus au sud et ceux en limite nord d’échantillonnage a été mise en évidence, suggérant peu de mélange génétique. Les allèles communs entre les individus échantillonnés évoquent une colonisation des individus de proche en proche depuis la mer Méditerranée. Des différences génétiques et de traits de vie ont été observées entre les individus échantillonnés en Manche, suggérant l’existence d’une barrière biogéographique au sein de cet environnement. La présence de conditions environnementales favorables constitue un atout majeur pour cette espèce prédatrice qui semble présenter une capacité d’acclimatation importante. L’ensemble des approches abordées dans le cadre de ces travaux ont permis d’apporter les premières données sur les traits de vie et la structure des populations d’une espèce à fort intérêt commercial dans une zone d’expansion récente en lien avec des modifications globales des conditions environnementales. / The gilthead seabream (Sparus aurata) is a sparidae species whose natural distribution stretches from Senegal to Ireland coasts, with its common habitat in the Mediterranean Sea. This species is still considered as rare in its northern limit of distribution. For a decade, the abundance of individuals caught in the northern limit (English Channel, Irish Sea and North Sea), has increased. This species is now a fishing resources in the English Channel. This phenomenon, in link with global warming, is explained by the northern expansion of its distribution range. No ecological data about this species in northern distribution range is currently published. Life history traits of S. aurata in relation to the spatio-temporal modification of its distribution range has been studied, through diet, growth and sea/coastal movement analysis. On the other hand, the population structure analysis of these northern populations has been done with a multi-marker approach coupling the genetics and otolith microchemistry.Analysis of the stomach contents of S. aurata at the northern range confirms an opportunistic diet with a high proportion of prey species from the genus Mytilus. The growth of individuals is lower than that observed on individuals in the Mediterranean Sea. This phenomenon is conditioned by environmental parameters (temperature, salinity) at the distribution range limit. Elemental composition of the otoliths allowed us to characterize the sea/coastal migrations during the first year of life, with a sea transition in winter and the occupation of coastal zones. A variability between individuals has been observed as a behavioral plasticity of individuals. This suggests the presence of nursery areas along the Atlantic and Channel Sea coasts. Otolith microchemistry and genetic approaches, combining the use of mitochondrial and microsatellites markers, have demonstrated the lack of structure within populations at the northern distribution range. This phenomenon matches with the recent population colonization. However, a differentiation was identified between the most southern individuals sampled and those at the northern sampling boundary, suggesting little genetic mixing. Common alleles between individuals suggest a “step by step” colonization of individuals from the Mediterranean Sea. Genetic and life history traits differences were observed between individuals sampled in the Channel Sea, suggesting a biogeographic barrier within this environment.Favorable environmental conditions are a major asset for this predatory species, which appears to have a huge acclimatization ability. All the various approaches discussed in this work have then made it possible to provide the first data on the life characteristics and the population structure of a species with a high commercial interest on the northern range of its distribution.

Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-05-22T17:32:45Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese__Aschenbrenner_versão_Definitiva.pdf: 1827049 bytes, checksum: 2b2e0b82d6dc856801226f7368d28b5b (MD5) / Made available in DSpace on 2017-05-22T17:32:45Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese__Aschenbrenner_versão_Definitiva.pdf: 1827049 bytes, checksum: 2b2e0b82d6dc856801226f7368d28b5b (MD5) Previous issue date: 2014-11-25 / O objetivo geral desta tese foi avaliar a conectividade entre ecossistemas costeiros e plataforma continental para a espécie L. alexandrei e estudar a utilização destas áreas em diferentes estágios do ciclo de vida para L. alexandrei e L. jocu na região costeira de PE. Para entender melhor a movimentação entre estas áreas, foram utilizados diferentes métodos combinados: (1) a estrutura etária e de tamanho de L. alexandrei foi determinada para áreas estuarinas (profundidades < 5m) e costeiras (profundidades entre 30 a 60 m) metros da plataforma continental; (2) a assinatura química de otólitos de indivíduos de L. alexandrei capturados em áreas estuarinas e costeiras foi analisada para evidenciar a variação ontogenética na permanência entre os diferentes habitats; (3) a presença em áreas estuarinas e recifes rasos adjacentes a costa em diferentes estágios do ciclo de vida foi detectada e quantificada para L. alexandrei e L. jocu através de censos visuais subaquáticos. Amostras biológicas (otólitos) de L. alexandrei foram coletadas através do acompanhamento de desembarques da pesca de Camboa em regiões estuarinas e pesca de rede e armadilhas em regiões costeiras entre o litoral dos estados de Pernambuco e Alagoas. As coletas foram realizadas durante três anos consecutivos (2010-2012). Otólitos de indivíduos juvenis e adultos foram extraídos, emblocados em resina, seccionados utilizando uma serra metalográfica e analisados inicialmente quanto à sua estrutura etária. Em uma segunda etapa, secções de otólitos foram analisadas com relação à sua assinatura química através de um espectrômetro de massa com ablação a laser. Observações subaquáticas foram realizadas em mangues (duas localidades) e recifes de coral adjacentes (três localidades) (a partir de 90 transectos de 10 x 2 m para cada localidade) durante os meses de novembro a março (2012- 13). Resultados da analise de distribuição etaria mostram que para áreas estuarinas indivíduos apresentaram idades de 0 a 4 anos, enquanto indivíduos coletados em áreas costeiras mais profundas foram mais velhos,entre 3 a 22 anos, indicando que uma mudança entre habitats ocorre aproximadamente entre idades 3 e 4. A frequência do tipo de borda ao longo de um ano utilizado para validar a deposição anual de anéis etários indica que, a formação da banda opaca ocorre no período chuvoso, entre abril e setembro. Dados de crescimento revelam que L. alexandrei possui um crescimento rápido durante os estágios iniciais de vida, atingindo em média 50% de seu tamanho assintótico com idade 2. Parâmetros da curva do modelo de crescimento de von Berlalanffy encontrados para L. alexandrei foram L∞ = 31 cm , k = 0.24, t0 = -1.26, r2 = 0.97. A taxa de mortalidade estimada para indivíduos coletados em áreas costeiras foi Z = 0.22 com sobrevivência de S = 0.78 year-1 . Para a analise microquímica dos otólitos foram medidos seis elementos: 7 Li, 24Mg, 55Mn, 59Co, 88Sr and 137Ba para indivíduos de L. Alexandrei. A analise de material recentemente depositado na borda de otólitos revelou que concentrações na razão elemento:Ca não variaram significativamente ao longo dos três anos testados. Similarmente, com exceção de dois elementos (Ba, Co), a razão elemento:Ca para indivíduos maiores habitando águas costeiras também foi estável, não apresentando diferenças para as diferentes regiões costeiras investigadas. Contrariamente, assinaturas químicas em otólitos de L. alexandrei de tamanhos similares provenientes da região estuarina e áreas costeiras foram distintas. Concentrações de Mn:Ca e Ba:Ca em otólitos foram ambos significativamente maiores para L. alexandrei coletados na região estuarina comparados a peixes coletados na região costeira adjacente, enquanto que para Sr:Ca uma tendência oposta foi observada. Dadas as diferenças pronunciadas na assinatura química entre áreas estuarina e costeiras, transectos de elemento:Ca foram construídos desde a região do núcleo até a margem em otólitos de indivíduos coletados em áreas costeiras para determinar o tempo de movimento (migração ontogenética) entre estuário e áreas costeiras. Concentrações de Mn:Ca e Ba:Ca mostraram um padrão semelhante ao esperado, com maiores concentrações para idades 1 e 2, com diminuição gradual para idades subsequentes. Este padrão sugere que espécimes de L. alexandrei começam a transição para habitats mais costeiros (e.g. menores concentrações de Mn e Ba) após a idade 2. Dados de observações subaquáticas corroboraram estes resultados, revelando que para ambas as espécies, indivíduos menores que 10 cm ocorrem exclusivamente em manguezais. Uma nítida mudança foi observada com um aumento de densidades para indivíduos acima de 10 cm em áreas recifais adjacentes. Para L. alexandrei a ocorrência de pos-assentantes, juvenis e subadultos foi registrada em manguezais enquanto que em recifes adjacentes apenas subadultos e adultos foram registrados. Padrão semelhante foi observado para L. jocu com individuos pos-assentantes, juvenis e subadultos em manguezais e juvenis e subadultos habitando recifes rasos adjacentes. Informações obtidas nesta Tese permitiram uma melhor compreensão dos padrões de crescimento e estrutura etária de L. alexandrei. Resultados sugerem ainda a movimentação ontogenética de L. alexandrei entre habitas costeiros e regiões costeiras mais profundas e permitem uma melhor compreensão da utilização de habitats costeiros em estágios iniciais de vida para as espécies de L. alexandrei e L. jocu. / Current objective of this thesis was to evaluate the connectivity among a shallow nursery area and deeper coastal ecossystems for L. alexandrei, and study utilization of such habitats in different life stages for L. alexandrei and L. jocu in the coastal areas of Pernambuco. In order to better understand movement between these areas, combined methods were applied: (1) initially age structure and size of L. alexandrei individuals were determined between estuarine (depths < 5 m) and deeper coastal areas (depths between 30 and 60 m); (2) otoliths microquimistry of L. alexandrei caught in estuarine and coastal areas were tested to evidence possible movement between these areas; (3) the utilization of mangroves and adjacent shallow reef areas in different life stages were studied through underwater visual census for L. alexandrei and L. jocu. Biological samples (otoliths) of L. alexandrei were collected through fishing landings of corral fisheries in estuarine areas and guillnets and traps for coastal areas between Pernambuco and Alagoas States. Data were collected during three consecutive years (2010- 2012). Otoliths of both juvenile and adult individuals were extracted, embedded in resin, sectioned with a low speed saw, then age structure were determined. In a second step, chemical concentrations of trace elements were analyzed in otolith sections using a laser ablation inductively coupled plasma mass spectrometer. Underwater observations (Total 90 transects of 10 x 2 m for each of the five locations) were performed along November to March (2012-13). Results show that inshore mangroves were comprised of individuals 0 to 4 years (mean: 2) while individuals in deeper reef environments were older (range: 3 to 22; mean: 8), indicating that an ontogenetic shift occurs at approximately age 3 or 4. Edge analysis was used to validate the annual deposition in the otoliths suggesting opaque growth rings were formed in the wet season between April and September. Growth data revealed that L. alexandrei display a faster growth in early life stages, reaching approximately 50% of its asymptotic size at age 2. Age at length data were used to predict growth rates of L. alexandrei using the von Bertalanffy growth model from where the following parameters were calculated: L∞ = 31 cm , k = 0.24, t0 = -1.26, r2 = 0.97. Mortality rates were estimated for coastal habitats, with Z = 0.22 and S = 0.78 year-1 . Concentrations of six trace elements were measure (7 Li, 24Mg, 55Mn, 59Co, 88Sr and 137Ba) in otoliths of L. alexadrei. Element:Ca ratios in the otoliths of juvenile and sub-adult L. alexadrei from estuaries were not significantly different among three consecutive years (2010, 2011 and 2012), suggesting that physicochemical conditions within the nursery investigated was temporally stable. Similarly, apart from two element (Ba, Co), element:Ca ratios for larger L. alexandrei inhabiting coastal waters were also similar. In contrast, otolith chemistry of similar sized L. alexandrei from estuarine and coastal areas was distinctly different (based on recently accreted material). Otolith Mn:Ca and Ba:Ca were both significantly higher for L. alexandrei collected in estuaries compared to fish from adjacent coastal reefs region, while the opposite trend was observed for Sr:Ca. Given the pronounced differences in otolith chemistry between estuarine and coastal areas, element:Ca transects were constructed from the core to margin of the otoliths for adults (age 7+) collected on reefs to determine the timing of movement (ontogenetic migration) from estuarine to coastal areas. Based on observed patterns of decline for both Mn:Ca and Ba:Ca, it appears that L. alexandrei begin to transition to more coastal habitats (i.e., lower element:Ca ratios) after age 2. Underwater observations indicate that for both species, individuals smaller than 10 cm occurred exclusively in mangroves. A distinct shift was observed with higher densities for individuals larger than 10 cm in adjacent shallow reef areas. For L. alexandrei mangroves registered occurrence of (postsettlers, juveniles and subadults) while for shallow reefs only (subadults and adults) were observed. A similar pattern was observed for L. jocu with individuals (postsettlers, juveniles and subadults) in mangroves and (juveniles and subadults) inhabiting shallow reefs. General information provided in this thesis allow a better understanding of size structure and growth pattern for L. alexandrei. Yet results suggest ontogenetic migration for L. alexandrei between shallow coastal and deeper marine habitats as well as a better understanding of habitat utilization in early life stages for L. alexandrei and L. jocu.

La connectivité écologique se mesure via l'estimation des mouvements réalisés par les organismes au cours de leurs vie. Parmi les outils existants, seule la microchimie des otolithes est capable de reconstruire les mouvements des poissons au cours de leur vie entière, notamment lors des migrations ontogénétiques. Son utilisation au sein des milieux oligotrophes et chimiquement peu contrastés tels que les récifs coralliens reste cependant marginale. C'est dans ce contexte que s'inscrit ce travail sur la microchimie des otolithes des poissons des récifs coralliens et mangroves de Nouvelle-Calédonie. Il se divise en deux parties. La première, méthodologique, est axée sur l'estimation du potentiel de l'outil microchimie des otolithes en Nouvelle-Calédonie, avec un chapitre sur la détermination des signatures multi-élémentaires caractéristiques des différents habitats de la Grande Terre et un chapitre sur l'étude de la relation entre la microchimie de l'environnement et celle des otolithes. La seconde partie se concentre sur l'application de la méthodologie précédemment développée a des thématiques écologiques, avec un chapitre sur le rôle des mangroves sur le cycle de vie et la distribution géographique d'une espèce de Lutjanidae, Lutjanus fulviflamma, et un chapitre centré sur les mouvements réalisés au cours de la vie de cette espèce. Les résultats démontrent que la microchimie des otolithes présente un potentiel élevé en Nouvelle-Calédonie avec un fort pouvoir de discrimination entre la mangrove et les récifs coralliens. La relation entre la microchimie de l'environnement et celle des otolithes est complexe et dépend fortement des espèces considérées. Cependant, les contrastes chimiques marqués de l'environnement se retrouvent au sein des otolithes. Les résultats démontrent une connexion forte entre les différents habitats pour L.fulviflamma, particulièrement entre la mangrove et les récifs coralliens avec une importance cruciale de la mangrove comme zone de nurserie. Trois différents patrons de mouvements entre habitats ont été identifiés. Cette diversité illustre une forte variabilité de la connectivité écologique entre les individus, avec pour certains d'entre eux, une fréquentation de l'habitat juvénile durant la phase adulte. / Ecological connectivity is defined by organism movements between habitats.Among the tools used to measure connectivity, otolith microchemistry is the only one able toreconstruct the fish movement throughout their entire lifetime, and thus include ontogeneticmigrations. However, it is seldom used in oligotrophic environments that typically show poorchemical contrasts such as coral reefs. In this context, this study focused on otolith microchemistryof coral reef and mangrove fishes of New Caledonia. This work comprises two parts. First, amethodological part to assess the potential of otolith microchemistry in New Caledonia, with onechapter on the determination of multi-elemental signatures of habitats from the Main Island and onechapter on the relationships between environmental and otoliths microchemistries. Second, thepreviously developed methodology was applied to ecological questions, with a chapter on theimportance of mangrove on the life cycle and the spatial distribution of a Lutjanidae, Lutjanusfulviflamma, and a chapter on the lifetime movement patterns of this species. Results revealed ahigh potential of otolith microchemistry in New Caledonia with a high power of discriminationbetween mangroves and coral reefs. Relationships between environmental and otolithmicrochemistries were complex and species-specific. However, strong chemical contrasts in theenvironment were traduced in the otoliths. Results showed a strong connection between differenthabitats for L. fulviflamma, in particular between mangroves and reefs with a crucial importance ofmangroves as nursery grounds. Three different patterns of lifetime movements among habitats wereidentified. This diversity illustrates a high variability of ecological connectivity patterns amongindividuals, with a possible return to the juvenile habitat during the adult stage.

Diet and movements in fishes are often logistically challenging to study. Trace element and stable isotope analyses have advanced these fields considerably, but are still constrained by methodological impediments, such as the tendency towards lethal sampling. Studying endangered fishes is particularly challenging as representative samples are difficult to obtain. However, the information gained from such studies is often critical to the recovery of endangered fishes as knowledge of life history attributes has the potential to greatly influence the success of management strategies. I tested the viability of using fin rays in fishes as a non-lethal approach to study diet and movement patterns over time. I then applied the methods I developed to study the life history of the critically endangered Goliath Grouper, Epinephelus itajara. Fin ray analyses have traditionally been used in age and growth studies, as well as in a limited number of projects that study the chemical constituents of the ray itself. Therefore, I first tested whether fin rays could be used as chronological recorders of chemical properties over time using a pseudo-experimental design. By using samples from various aquaria, I had documentation of the time of capture of every animal used. Based on the assumption that the otolith in fishes represents a conserved, chronological matrix, I compared trace element concentrations between the otolith and the fin ray of each individual. In addition I tested whether stable isotope values of δ13C and δ15N differed between the wild and captive life phases of each individual. Divalent ions and positively-charged transition metals (e.g., Fe, Co) in particular showed strong associations between the two structures, suggesting conservation of material. Stable isotope values of δ13C and δ15N differed between the wild and captive life phases in most of the fishes sampled, also suggestive of conserved matrices. I then tested and modeled the differences in δ15N values over time between the populations of Goliath Groupers on the west and east coasts of Florida. In general, individuals on the west coast had lower overall values and a larger difference between juvenile and adult values. The mechanism that caused the differences between coastal populations may have been an artifact of the environment, rather than different feeding behaviors. Last, I investigated different nursery habitats for Goliath Groupers in southwestern Florida. I characterized juvenile nurseries based on the chemical fingerprints of trace elements within the inorganic matrix of the fin rays. Groupings based on these fingerprints were surprisingly accurate and can be used to identify essential nursery habitat for the species in years to come. This research demonstrated the efficacy of novel techniques that were used to gather information on the life history of a critically endangered fish in the state of Florida. The results can be used to influence management strategies in the future, particularly with regard to nursery habitat use.

La gestion des ressources alimentaires doit passer par un équilibre entre activités humaines et une exploitation raisonnée de ces ressources. Sur l'île de La Réunion, la réserve naturelle marine œuvre pour le maintien des populations de poissons traditionnellement exploitées comme le mérou macabit (Epinephelus merra, Serranidae) ou d'intérêt écologique (Acanthurus triostegus, Acanthuridae, et Plectroglyphidodon imparipennis, Pomacentridae). Pour mieux appréhender leur phase de vie larvaire souvent méconnue, la microchimie des otolithes a été utilisée pour retracer la vie des poissons dans un objectif appliqué à la gestion. Nos résultats ont permis de différencier la population de macabit à La Réunion en 3 groupes d'histoires de vie larvaires différentes sur un gradient nord-sud, à partir de fortes variations en baryum, un élément trace provenant de l'environnement. Ces variations sont retrouvées également chez A. triostegus et P. imparipennis, principalement issues d'évènements cycloniques. Des sources de cet élément ont été identifiées dans des eaux du socle basaltique de l'île de La Réunion, mais aussi à l'échelle de l'océan Indien, aux Maldives, Juan De Nova et Europa. Le baryum s'est ainsi révélé être un élément trace à privilégier pour l'analyse de l'histoire de vie des poissons récifaux et pour révéler les caractéristiques spatiales et temporelles de la structure de leurs populations à l'échelle de La Réunion et dans l'océan Indien. Des études complémentaires biologiques, chimiques et génétiques sont néanmoins nécessaires afin d'aboutir à des connaissances permettant d'adapter des mesures de gestion aux cycles biologiques des espèces. / Ood resources must managed between human activities and sustainable exploitation. On Reunion Island, the marine park works more specifically to maintain fish populations with high commercial value, regularly exploited by traditional fishermen, such as the grouper Epinephelus merra (Serranidae), Acanthurus triostegus (Acanthuridae) and Plectroglyphidodon imparipennis (Pomacentridae) which pelagic larval phase remains unknown. To better understand this phase, the otolith microchemistry was used to trace the life histories for management purposes. Our results allowed differentiating grouper population in Reunion in 3 different groups of larval life histories, using barium concentration in their otoliths which can be enriched in the environment. These chemical changes are also found in A. triostegus and P. imparipennis. In the northern reef area (Saint-Gilles and Saint-Paul), these variations are observed significantly mainly during cyclonic events. Natural sources of this element could be identified locally in groundwater collected in the porous basaltic basement of the Reunion, but also at the regional level, where other individuals were collected in the Indian Ocean (Maldives Juan De Nova, Europa). Therefore barium has proven to be an interesting trace element for the analysis of the life story of reef fish, and a tool to reveal the spatial and temporal characteristics of their populations across Reunion structure but also in the Western Indian Ocean. Nevertheless biological, chemical and genetic studies are necessary to complete the knowledge and adapt management measures to the biological cycles of the species.

No description available.

La dispersion, caractérisée par les mouvements d’individus dans l’espace et dans le temps, conduit à la production d’un flux de gènes et permet la connectivité des populations. Comprendre les facteurs qui façonnent les flux de gènes et la structuration des populations est d’une importance capitale pour améliorer les pratiques de gestion et de conservation des espèces. Celles caractérisées par une anadromie facultative, telles que la truite commune (Salmo trutta L.), sont des modèles de choix pour étudier le rôle de la diversité écotypique et comportementale, sous l’effet des activités anthropiques, sur le fonctionnement des populations. En utilisant la génétique des populations cette thèse se propose donc d’analyser la structuration des populations de la truite commune dans le fond du Golfe de Gascogne mais également de déterminer l’influence combinée de la dispersion de la truite de mer, de son comportement reproducteur et des activités anthropiques (repeuplements, transport de reproducteur) sur leur fonctionnement. Cette thèse aborde également la contribution des populations de truites communes (via leur origine natale) au stock de truites de mer capturées par la pêche professionnelle, sur le même site d’étude, en couplant de la génétique des populations et de la microchimie des otolithes. Nos résultats montrent une structuration génétique forte des populations de truite commune avec la présence de sept populations distinctes dans le bassin de l’Adour. Ceci semble être en partie expliqué par un comportement marqué de fidélité au site de naissance des truites de mer, couplé à un mouvement directionnel de celles-ci du sud (Espagne) vers le nord qui ne semble pas résulter en une dispersion effective (i.e. mouvement suivi d’une reproduction). En outre, les repeuplements récents, semblent impacter faiblement la structuration génétique des populations sauvages. Certains flux de gènes détectés localement semblent être dus à d’autres activités anthropiques, telles que le transport de reproducteurs. Les truites de mer capturées par la pêche professionnelle proviennent majoritairement de la population du gave d’Oloron et peu des populations des Nives et du Gave de Pau. La raison pourrait se trouver en premier lieu dans le fait que le Gave de Pau est fortement impacté par la présence de barrières à la migration et en second lieu dans les différences phénotypiques (taille plus petite) présentées par les truites de mer des Nives, par rapport à celle des gaves. Ceci suggère donc une différenciation de cette population et peut expliquer que la pêche professionnelle les capture dans une moindre proportion. Cette thèse a d’autre part pu démontrer les difficultés dans l’assignation d’une origine natale via la génétique lorsque les signatures génétiques sont relativement proches. Elle confirme l’utilité d’un couplage génétique des populations - microchimie des otolithes pour assigner des individus à leur origine natale à une échelle plus fine que le bassin. Les résultats obtenus au cours des trois années de thèse ont permis la détermination de populations génétiquement distinctes dont l’une contribue très largement à l’activité de pêche professionnelle. Ces populations peuvent être considérées comme de potentielles unités de gestion qui pourront servir de base à l‘élaboration de plans de gestion et de conservation. La meilleure compréhension de la biologie et du fonctionnement de la truite commune, et de l’impact des activités anthropiques sur la structuration des populations, acquise lors de cette thèse, pourra également permettre d’améliorer la prise de décisions des gestionnaires locaux pour la conservation et la gestion des populations de truites communes. / Dispersal, characterized by the movements of individuals in space and time leading to gene flows, allows populations to connect. Understanding factors shaping gene flow and population structure is vital to improve management and conservation practices of species. Those characterized by a partial anadromy, such as brown trout (Salmo trutta L.), are models of choice to study the role of ecotypic and behavioral diversity, under anthropic activities on population functioning. By using population genetics, this theses proposes to analyse population structure of brown trout in the Bay of Biscay, but also to determine the combined influence of sea trout dispersal, its reproductive behavior, and anthropic activities (stocking, transport of spawners) on their functioning. This thesis also addresses the contribution of brown trout populations (natal origin) on sea trout stock captured by professional fisheries, on the same study site, by coupling population genetics and otolith microchemistry. Results show a strong hierarchical structure of Brown trout population with seven distinct population detected in Adour basin. This seems to be explained a high site fidelity movement of sea trout together with a directional movement of sea trout from South (Spain) to North. This directional movement did not result into effective dispersal (i.e. movement followed by reproduction). Furthermore, a limited contemporary impact of stocking on genetic structure of wild population is observed. A few cases of inter-population gene flow detected seems to be explained by wild population management, particularly transport of spawners. The majority of sea trout captured by professional fisheries come from Gave d’Oloron and few from Nives and Gave de Pau. The reason is that Gave de Pau is impacted by migration barriers. And also that sea trout from Nives have phenotypic differences (smaller length) from sea trout originated from gaves. This suggest a differentiation of this population and can explained that professional fisheries capture them in smaller proportion.On the other hand, this thesis have been shown the difficulties to assign natal origin by using genetics when population are closed genetically. This confirm the usefulness to coupling population genetics and otolith microchemistry together to assign individuals to their natal origin at a finer scale than basin.Results obtained during these three years of thesis have made it possible the determination of distinct populations one of which contribute in majority of professional fisheries activities. These populations can be considered like potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans. The better understanding of brown trout biology and functioning, and the impact of anthropic activities on population structure, obtained in this thesis, can also improve the decision-making of local managers for brown trout population conservation and management.