Understanding the biogeography of reef fish assemblages is paramount to reef conservation, management, and conducting appropriate population survey designs. Reef fish assemblages are a multispecies complex of reef-associated fish and are shaped by multiple environmental and biological factors (e.g. temperature, depth, benthic habitat, and topographic relief), which determine the species constituents residing in an area. Assemblages typically change with latitude where the number of families, genera, and/or densities of species specific to warmer climates decrease poleward into colder climate regimes. The Florida Reef Tract (FRT) extends for 595 km from the Dry Tortugas in the south-west to Martin County in the north, crossing a sub-tropical to temperate climate transition. This study investigates the biogeography of reef fish assemblages throughout the FRT to determine if they correspond to previous regional delineations that were primarily based on coastal geomorphology. Multivariate density analyses show that depth, habitat, relief, and region are major factors in determining the assemblages. Four main ecoregions were evident based on depth, benthic habitat, relief and latitudinal region: Dry Tortugas (DT), Florida Keys (FK), Southeast mainland (SE), and Bahamas Fracture Zone (BF). DT split into four biogeographic assemblage regions primarily based on depth, and relief. FK split into five biogeographic assemblage regions with a sixth extending through Broward County primarily based on depth, habitat type, and relief. SE split into four biogeographic assemblage regions primarily based on depth, and region. BF split into three biogeographic assemblage regions primarily based on depth, and region. These sixteen assemblages represent the current composition of reef fish based on four factors. Numerous other factors also affect reef fish assemblages (e.g. past and present fishing pressure, mangrove nursery habitat, and coral death) that were not part of the analysis but are discussed. The final reef fish assemblage regions were associated with previous benthic habitat maps in order to view their spatial extent. Having a map of current biogeographic reef fish assemblages serves as a baseline and allows more accurate management and monitoring of future reef fish populations.

L’estimation de la diversité et de l’abondance des espèces de poisson est fondamentale pour comprendre la structure des communautés et la dynamique des récifs coralliens. Les observations sont généralement obtenues par des recensements visuels en scaphandre autonome (UVC). Ces informations peuvent également être obtenues de manière originale grâce aux observations issues des techniques vidéo sous-marines modernes sans plongeur qui permettent des couvertures spatiales et temporelles accrues.La première phase de ce travail de thèse synthétise l’ensemble des travaux ayant été effectués avec des techniques vidéo entre 1952 et 2012. La seconde phase, présente deux systèmes vidéo rotatifs complémentaires, utilisés pour étudier la diversité de l’ichtyofaune et des habitats marins dans le lagon de Nouvelle-Calédonie : le STAVIRO (pour « STAtion VIdéo ROtative ») et le MICADO (pour « Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine »). La troisième phase de ce travail consiste à comparer ces systèmes vidéo aux UVC puis à examiner l’effet « observateur » inhérent aux techniques vidéo rotatives. Il résulte de cette étude que : (i) les observations des communautés de poissons par UVC et STAVIRO différaient significativement, (ii) la richesse spécifique etla densité des espèces de grande taille n'étaient pas significativement différentes entre les techniques, (iii) la diversité et la densité des espèces de petite taille étaient plus élevés avec les UVC; (iv) la densité des espèces pêchées était plus élevée avec les STAVIRO et (v) seuls les UVC ont détecté des différences de structure des assemblages en fonction du type de récif. L’étude de l’effet « observateur » a montré que sur une liste d’espèces définie, les dénombrements et les identifications des individus peuvent être considérées comme similaires entre observateurs ayant une expérience suffisante (> 6 mois). La dernière phase de ce travail a permis d’appliquer la technique MICADO à l’étude des variations temporelles del’ichtyofaune d’un site corallien à l’échelle de la journée. Elle a permis de mettre en évidence des variations cycliques journalières en fonction de l’heure et de la marée et des « profils type » de variations ont pu être identifiés pour certains groupes d’espèces. Ce travail de thèse permet ainsi de participer au développement de nouvelles techniques d’observations complémentaires des techniques traditionnelles afin d’enrichir les connaissances du fonctionnement et de la dynamique des écosystèmes coralliens. / Estimating diversity and abundance of fish is fundamental for the understanding of community structure and dynamics of coral reefs. Observations are generally gathered using Underwater VisualCensus (UVC). These informations can also be collected by underwater video techniques involving no diver and allowing a high spatial and temporal coverage. The first part of this PhD thesis is a review ofpublications using underwater video techniques between 1952 and 2012. The second part present two rotating video systems used to study the diversity of ichthyofauna and habitats in the lagoon of NewCaledonia: the STAVIRO (for "STAtion VIdeo ROtative") and the MICADO (for "Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine"). The third part of this work is acomparison of these techniques with UVCs and an analysis of the “observer effect” for the rotating video techniques. The comparison between rotating video systems and UVC showed that: (i) fish communitydata collected by UVC and by STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of smallspecies were higher for UVC; (iv) density of fished species was higher for STAVIRO; and (v) only UVC detected significant differences in fish assemblages structure across reef type. The comparison of fishcounts obtained from the same videos by different observers showed that for a defined list of species, estimates of species richness and total abundance can be considered as similar between observers withsufficient experiences (> 6 months). The last part of this PhD is an application of rotating video techniques to the study of daily temporal variations of the ichthyofauna. Daily variations were observed depending onthe time of day and the tidal state and typical patterns of variations have been described for some species groups. The outcomes of this work bring original insights of new techniques complementary to traditionaltechniques in order to enhance our understanding of the functioning and dynamic of coral reef.

La couleur est un trait biologique essentiel et très variable qui permet à un organisme d'être adapté à son environnement biotique et abiotique. De multiples gènes influent sur la couleur ; leur évolution a été étudiée ici chez les Vertébrés en lien avec les duplications de génome survenues dans cette lignée . Alors que l'essentiel des gènes sont perdus lors de la rediploïdisation suivant une duplication totale de génome, ces travaux montrent que les gènes de la pigmentation appartiennent à des fa milles de gènes qui sont en moyenne plus retenues que le reste du génome . Ceci est particulièrement vrai pour les poissons Téléostéens, cette expansion du répertoire de gènes de pigmentation pouvant être en lien avec la grande diversité de cellules pigmenta ires et de patrons de pigmentation observés chez ces animaux . Par ailleurs, l'étude de la pigmentation d'un organisme modèle émergent, le poisson -clown Amphiprion oellaris, a été réalisée dans le cadre de cette thèse . La nature cellulaire de la bande blanche de ce poisson a été déterminée et a permis l'identification - d'un nouveau gène présent presque exclusivement chez les poissons Actinoptérygiens , probablement acquis par transfert horizontal, et impliqué dans le développement d'un type de cellules pigmentaires, les iridophores . Enfin, l'acquisition de la pigmentation au cours du développement du poisson -clown A. ocellaris, un poisson corallien au cycle de développement marqué par une métamorphose, a été étudiée en rapport avec la signalisation thyroïdienne, qui joue un rôle majeur au cours du développement des Vertébrés . / Color is a key biological trait that allows individuals to adapt to their biotic and abiotic environment, and many genes have been shown to play an essential role in color acquisition in vertebrates. In this work, the consequences on this specifie set of genes of the whole-genome duplications that occurred during vertebrate evolution were investigated. Whereas most genes a re lost after a w hole- genome duplication event, this work shows that pigmentation genes and other genes within their families have been more retained compared to the average observed genome retention. This was particularly the case for the teleost-specific whole-genome duplications . Hence, this high retention rate could  be related to the high pigmentation diversity observed in the teleost fish lineage, both  in terms of patterns and of pigment cell types . In addition, during this PhD thesis, pigmentation in an emerging model organism, the clownfish Amphiprion ocellaris, was investigated. The white color in clownfish was shawn to be due to specifie pigment cells,  iridophores, and new iridophore genetic markers were detected . One such marker is almost exclusively restricted to ray-finned fish and could have been acquired through a horizontal gene transfer event that occurred at the onset of the evolution of this lineage. Last, in this work, the genetic basis of pigmentation acquisition was scrutinized during the development of clownfish A. ocellar is, and especially during metamorphosis - a major life history transition  in coral  reef  fish . In particular, the  deployment  during  development  of thyroid  hormone signaling  which is a key pathway in metamorphosis regulation in vertebrates  was examined.

This thesis focuses on the investigation of reef communities of the Saint Peter and Saint Paul´s Archipelago (SPSPA) across an euphotic/mesophotic depth gradient. Sampling was performed on shallow and mesophotic areas (0 to 90 m depth) using SCUBA and a Remotely Operated Vehicle (ROV). The present work is composed of four chapters: Chapter 1 deals with the quantitative assessment of reef fish communities, which were divided in three distinct communities associated with different depth strata. Clear shifts in habitat use and in size-frequency distributions were recorded for some species. Abundance of black-corals and depth were the most important factors affecting the structure of fish communities, with a clear association of fish with branching black-corals in the mesophotic zone. Chapter 2 presents the first detailed qualitative assessment of benthic communities of the SPSPA. The influence of biotic and abiotic variables shaping the structure of the benthic communities was evaluated. A total of 77 benthic taxa belonging to six major functional groups were recorded. Macroalgae was the richest group (41 infrageneric taxa), with 17 new records for the SPSPA. Turf algae were the most abundant group on both shallow and mesophotic reefs. Two distinct communities were detected: a shallow one composed primarily by the zoanthid Palythoa caribaeorum (Duchassaing and Michelotti, 1861), the fleshy alga Caulerpa racemosa (Forsskål) J. Agardh, crustose coralline algae (CCA) and Bryopsis spp., and another deeper community dominated by CCA, bryozoans and scleractinian corals. Abiotic variables were the most important predictors of benthic community structure. Chapter 3 brings information on abundance, distribution size and associated fauna (epibionts) of black-corals. Although two species of black-corals, Tanacetipathes hirta (Gray, 1857) and T. thamnea (Warner, 1981), are known to occur in the SPSPA, they are undistinguishable underwater. Epibiosis, mainly by zoanthids and entanglement by fishing monofilament were important factors negatively affecting the health of black-coral colonies. Black-corals were intensively used as refuge by reef fish, especially by the endemic oblique butterflyfish Prognathodes obliquus (Chaetodontidae). A single black-coral colony repeatedly visited and monitored for ten years showed a decrease in vitality since the first observation, mainly related to fouling by algal detritus and entanglement by fishing monofilaments. Chapter 4 discusses the ecology (abundance, distribution and habitat preferences) of the fireworm Hermodice carunculata, a major predator on mesophotic zone of SPSPA. A total of 278 individuals of bearded fireworm were observed, with significant difference in abundance between euphotic and mesophotic zones. A direct association of H. carunculata with black-corals (Tanacetipathes spp.), the scleractinian Madracis decactis and depth was found. A final session with concluding remarks wraps up information on the ecology of Mesophotic Reef Ecosystems highlighting their possible importance for the stability and persistence of reef fish and benthic communities of the SPSPA, which are under threat of overfishing and climate change, thus requiring urgent protective measures. / O tema central desta tese é estudar a ecologia de comunidades recifais ao longo do gradiente de profundidade no Arquipélago São Pedro e São Paulo (ASPSP), com ênfase nos Ecossistemas Recifais Mesofóticos (ERMs). As amostragens foram realizadas da superfície até a zona mesofótica (0 a 90 m de profundidade), utilizando SCUBA e Veículos Submersíveis de Operação Remota (VSORs). Esta tese é composta por quatro capítulos. No Capítulo 1 foi realizado uma avaliação quantitativa das comunidades de peixes, as quais formaram três comunidades distintas associadas aos diferentes estratos de profundidade e ao uso de diferentes hábitats de acordo com mudanças ontogenéticas (tamanho do corpo). Corais-negros e profundidade foram os fatores mais importantes na estruturação das comunidades de peixes, com uso intenso dos corais-negros por peixes na zona mesofótica. O Capítulo 2 apresenta a primeira avaliação qualitativa das comunidades bentônicas do ASPSP, além de uma avaliação da influência de variáveis bióticas e abióticas na estruturação das comunidades. Foram registrados 77 táxons bentônicos pertencentes a seis grupos. Macroalgas foi o grupo mais rico (41 táxons), com 17 novos registros para o ASPSP. Algas formadoras de tufos (turf) constituíram o grupo mais abundante em ambos os ambientes, eufótico e mesofótico. Foram observadas duas comunidades distintas: uma superficial composta principalmente pelo zoantídeo Palythoa caribaeorum, a pela alga Caulerpa racemosa carnuda, algas calcárias incrustantes (CCA) e Bryopsis spp, e outra mais profunda dominada por CCA, briozoários e corais escleractíneos. As variáveis abióticas, particularmente profundidade e luz, foram mais importantes na estrutura da comunidade bentônica. O Capítulo 3 traz informações sobre a abundância, distribuição, tamanho e vitalidade de corais-negros. Duas espécies de corais-negros, Tanacetipathes hirta (Gray, 1857) e T. thamnea (Warner, 1981), foram identificadas. Epibiose por zoantídeos e estrangulamento por monofilamentos afetaram negativamente as colônias de coral negro, uma delas monitorada durante dez anos. Esta última apresentou uma diminuição da vitalidade devido principalmente à presença de algas e estrangulamento por monofilamento. Corais-negros formam um grupo-chave na zona mesofótica do ASPSP, sendo intensamente utilizados como hábitat por diversos peixes recifais, principalmente espécies endêmicas (e.g., o peixe-borboleta Prognathodes obliquus). O Capítulo 4 aborda a ecologia do principal predador de invertebrados bentônicos na zona mesofótica do ASPSP, o verme-de-fogo Hermodice carunculata, descrevendo sua abundância e distribuição batimétrica e discutindo seu potencial em impactar as comunidades bentônicas, especialmente os corais escleractínios e os corais-negros na zona mesofótica do ASPSP. Observou-se um total de 278 indivíduos, com diferença significativa na abundância entre as zonas eufótica e mesofótica. Foi encontrada uma associação direta entre H. carunculata e 1) corais-negros (Tanacetipathes spp), 2) o coral escleractíneo Madracis decactis e 3) profundidade. Sugere-se aqui que os ecossistemas mesofóticos são essenciais para a estabilidade para as comunidades recifais eufóticas do ASPSP, tornando urgente a necessidade de novos estudos, principalmente com foco no potencial impacto da pesca e mudanças climáticas.

Les parasites sont une partie très importante des écosystèmes, néanmoins, dans certains cas tels que l’aquaculture ils causent des épidémies. Dans cette thèse j’ai étudié les interactions hôte-parasite chez les poissons coralliens, dans les milieux naturels et les milieux aquacoles. J’ai étudié l’arrangement des communautés de 13 espèces de monogènes de 34 espèces de poissons papillon dans l’Indo-Pacifique. Les résultats montrent qu’il existe un patron de distribution stable des espèces, ce qui, combiné avec les résultats de l’étude biogéographique, suggère que la spécificité parasitaire observée a pu se développer tout au long des épisodes biogéographiques passés. Notamment, seule une espèce, Chaetodon lunulatus, n’est jamais parasitée. J’ai étudié le mucus des poissons qui est décrit comme la première ligne de défense contre des agressions externes, pour analyser quels facteurs de C. lunulatus pourraient être reliés à l’absence des parasites. Le microbiome et le métabolome du mucus branchial des poissons papillons montrent une grande diversité. C. lunulatus présente une plus grande abondance de Fusobactéries qui est corrélée avec une surexpression de peptides pouvant dériver de la β-hémoglobine. La purification, la synthèse et l’évaluation des activités antiparasitaires des peptides sont en cours au laboratoire. J’ai aussi étudié l’utilisation des plantes médicinales comme alternative à des traitements chimiques dans l’aquaculture. J’ai testé l’activité antibactérienne et immunostimulatrice de plusieurs plantes et algues polynésiennes. L’algue rouge Asparagopsis taxiformis montre de fortes activités antibactériennes sur Vibrio harveyi et Tenacibaculum maritimum et induit une augmentation de l’expression de deux gènes liés à l’immunité chez Platax orbicularis. / Fish parasites are an important part of ecosystems, however, in certain cases such as in aquaculture they can cause severe disease outbreaks. In this thesis I have studied host-parasite interactions in coral reef fishes, both in the natural and culture environments. I have studied the distribution of 13 dactylogyrid species from 34 butterflyfishes in the Indo West-Pacific. Composition of dactylogyrid communities was host specific and together with the biogeography results, where a turnover in the main Haliotrema species was observed, suggest that parasite specificity might result from host-parasite coevolution derived from past biogeographical episodes. Only one butterflyfish species, Chaetodon lunulatus, was never found parasitized by gill monogeneans. I have studied the butterflyfish mucus, which is the first barrier against pathogens, to investigate the C. lunulatus factors that might be related to the monogenean absence. Butterflyfish gill microbiome and metabolome revealed a high diversity. C. lunulatus presented a significantly higher abundance of Fusobacteria which was correlated to a higher expression of potentially derived β-hemoglobin peptides. Synthesis and evaluation of the peptide antiparasitic activities are being performed in the laboratory. I have also studied the use of medicinal plants as an alternative to chemotherapy in fish aquaculture. I investigated the antibacterial and immunostimulant activities of several local Polynesian plants and algae, and I found that Asparagopsis taxiformis displayed a potent antibacterial activity against Vibrio harveyi and Tenacibaculum maritmum and increased expression of two immune-related genes in Platax orbicularis.

Made available in DSpace on 2015-04-17T14:55:28Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 2453210 bytes, checksum: 30faa7ddf8d520d8e3c100c3296d8a2b (MD5) Previous issue date: 2011-02-24 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Several types of mechanisms can influence community structure of fishes in marine ecosystems, such as larval recruitment, interaction between species, abiotic factors, composition and percent cover of benthic organisms, mainly providing a relationship of habitat complexity with higher abundance and structural diversity. In this context, this study aimed to survey the reef fish fauna of coastal habitats located in the Parque Estadual Marinho Areia Vermelha, with emphasis on habitat characteristics, distribution patterns and conservation aspects recorded species in the area. The study site was divided into sampling stations according to the history of tourism activity: Areia Vermelha (AV - longer visiting history), Areia Dourada (AD - recent visiting history) and No Visit (SV - adjacent area - no visiting history). The stations were sampled by the method of stationary visual census in free-diving, with the average duration of 15 minutes and between December 2009 and April 2010, December 2010 and January 2011. Among the types of substrate coverage analyzed, there was a dominance of sessile invertebrates in AD and macroalgae in AV and SV. during the 150 censuses, a total of 6141 specimens were recorded, including by 55 species, distributed in 26 families. Labridae (Scarinae) was the family with highest abundance and Haemulidae the one with highest species richness. The species that yielded the largest number of individuals on the macroalgae environments were Sparisoma axillare, Abudefduf saxatilis, Acanthurus chirurgus, Haemulon parra and Halichoeres brasiliensis, while the reefs were Sparisoma axillare, Abudefduf saxatilis, Acanthurus chirurgus, Scarus zelindae and Halichoeres brasiliensis. Most individuals were found in the juvenile stage. With respect to trophic structure, most sighted individuals were grouped in the category Non-Territorial Herbivores. The environments analyzed in this study proved to be important for juvenile individuals of different species as well as for endangered fishes, indicating the importance of their conservation for the survival of these species. / Muitos mecanismos podem influenciar a estrutura da comunidade de peixes em ambientes marinhos, tais como o recrutamento larval, interação entre as espécies, fatores abióticos, composição e percentagem de cobertura de organismos bênticos, conferindo principalmente à complexidade do habitat uma relação com maior abundância e diversidade estrutural. Diante deste contexto, o presente trabalho objetivou inventariar a fauna de peixes recifais do Parque Estadual Marinho Areia Vermelha, com ênfase na caracterização do habitat, padrões de distribuição e aspectos da conservação das espécies registradas no Parque. A área de estudo foi dividida em estações de coleta de acordo com o histórico de turismo: Areia Vermelha (AV histórico antigo de visitação), Areia Dourada (AD histórico recente de visitação) e Sem Visita (SV área adjacente sem histórico de visitação). As estações foram amostradas pelo método do censo visual estacionário, em mergulho livre, com duração média de 15 minutos e entre dezembro de 2009 a abril de 2010, dezembro de 2010 e janeiro de 2011. Dentre os tipos de cobertura de substrato analisados, houve dominância dos invertebrados sésseis em AD e de macroalgas em AV e SV. Dos 150 censos realizados, foi registrado um total de 6.141 espécimes, representados por 55 espécies e distribuídos em 27 famílias. Labridae (Scarinae) foi o grupo com maior abundância e Haemulidae a família com maior riqueza de espécies. As espécies que perfizeram o maior número de indivíduos nos ambientes de macroalga foram Sparisoma axillare, Abudefduf saxatilis, Acanthurus chirurgus, Haemulon parra e Halichoeres brasiliensis, enquanto nos recifes foram Sparisoma axillare, A. saxatilis, A. chirurgus, Scarus zelindae e H. brasiliensis. A maioria dos indivíduos foram encontrados no estágio juvenil. Em relação às categorias tróficas, a maior parte dos indivíduos avistados foi agrupada na categoria Herbívoros não territorialistas. Os ambientes analisados no presente estudo mostraram ser importantes para indivíduos jovens de variadas espécies, bem como para peixes considerados ameaçados de extinção, o que remete a importância da conservação de tais ambientes para a sobrevivência destas espécies.

This thesis focuses on the investigation of reef communities of the Saint Peter and Saint Paul´s Archipelago (SPSPA) across an euphotic/mesophotic depth gradient. Sampling was performed on shallow and mesophotic areas (0 to 90 m depth) using SCUBA and a Remotely Operated Vehicle (ROV). The present work is composed of four chapters: Chapter 1 deals with the quantitative assessment of reef fish communities, which were divided in three distinct communities associated with different depth strata. Clear shifts in habitat use and in size-frequency distributions were recorded for some species. Abundance of black-corals and depth were the most important factors affecting the structure of fish communities, with a clear association of fish with branching black-corals in the mesophotic zone. Chapter 2 presents the first detailed qualitative assessment of benthic communities of the SPSPA. The influence of biotic and abiotic variables shaping the structure of the benthic communities was evaluated. A total of 77 benthic taxa belonging to six major functional groups were recorded. Macroalgae was the richest group (41 infrageneric taxa), with 17 new records for the SPSPA. Turf algae were the most abundant group on both shallow and mesophotic reefs. Two distinct communities were detected: a shallow one composed primarily by the zoanthid Palythoa caribaeorum (Duchassaing and Michelotti, 1861), the fleshy alga Caulerpa racemosa (Forsskål) J. Agardh, crustose coralline algae (CCA) and Bryopsis spp., and another deeper community dominated by CCA, bryozoans and scleractinian corals. Abiotic variables were the most important predictors of benthic community structure. Chapter 3 brings information on abundance, distribution size and associated fauna (epibionts) of black-corals. Although two species of black-corals, Tanacetipathes hirta (Gray, 1857) and T. thamnea (Warner, 1981), are known to occur in the SPSPA, they are undistinguishable underwater. Epibiosis, mainly by zoanthids and entanglement by fishing monofilament were important factors negatively affecting the health of black-coral colonies. Black-corals were intensively used as refuge by reef fish, especially by the endemic oblique butterflyfish Prognathodes obliquus (Chaetodontidae). A single black-coral colony repeatedly visited and monitored for ten years showed a decrease in vitality since the first observation, mainly related to fouling by algal detritus and entanglement by fishing monofilaments. Chapter 4 discusses the ecology (abundance, distribution and habitat preferences) of the fireworm Hermodice carunculata, a major predator on mesophotic zone of SPSPA. A total of 278 individuals of bearded fireworm were observed, with significant difference in abundance between euphotic and mesophotic zones. A direct association of H. carunculata with black-corals (Tanacetipathes spp.), the scleractinian Madracis decactis and depth was found. A final session with concluding remarks wraps up information on the ecology of Mesophotic Reef Ecosystems highlighting their possible importance for the stability and persistence of reef fish and benthic communities of the SPSPA, which are under threat of overfishing and climate change, thus requiring urgent protective measures. / O tema central desta tese é estudar a ecologia de comunidades recifais ao longo do gradiente de profundidade no Arquipélago São Pedro e São Paulo (ASPSP), com ênfase nos Ecossistemas Recifais Mesofóticos (ERMs). As amostragens foram realizadas da superfície até a zona mesofótica (0 a 90 m de profundidade), utilizando SCUBA e Veículos Submersíveis de Operação Remota (VSORs). Esta tese é composta por quatro capítulos. No Capítulo 1 foi realizado uma avaliação quantitativa das comunidades de peixes, as quais formaram três comunidades distintas associadas aos diferentes estratos de profundidade e ao uso de diferentes hábitats de acordo com mudanças ontogenéticas (tamanho do corpo). Corais-negros e profundidade foram os fatores mais importantes na estruturação das comunidades de peixes, com uso intenso dos corais-negros por peixes na zona mesofótica. O Capítulo 2 apresenta a primeira avaliação qualitativa das comunidades bentônicas do ASPSP, além de uma avaliação da influência de variáveis bióticas e abióticas na estruturação das comunidades. Foram registrados 77 táxons bentônicos pertencentes a seis grupos. Macroalgas foi o grupo mais rico (41 táxons), com 17 novos registros para o ASPSP. Algas formadoras de tufos (turf) constituíram o grupo mais abundante em ambos os ambientes, eufótico e mesofótico. Foram observadas duas comunidades distintas: uma superficial composta principalmente pelo zoantídeo Palythoa caribaeorum, a pela alga Caulerpa racemosa carnuda, algas calcárias incrustantes (CCA) e Bryopsis spp, e outra mais profunda dominada por CCA, briozoários e corais escleractíneos. As variáveis abióticas, particularmente profundidade e luz, foram mais importantes na estrutura da comunidade bentônica. O Capítulo 3 traz informações sobre a abundância, distribuição, tamanho e vitalidade de corais-negros. Duas espécies de corais-negros, Tanacetipathes hirta (Gray, 1857) e T. thamnea (Warner, 1981), foram identificadas. Epibiose por zoantídeos e estrangulamento por monofilamentos afetaram negativamente as colônias de coral negro, uma delas monitorada durante dez anos. Esta última apresentou uma diminuição da vitalidade devido principalmente à presença de algas e estrangulamento por monofilamento. Corais-negros formam um grupo-chave na zona mesofótica do ASPSP, sendo intensamente utilizados como hábitat por diversos peixes recifais, principalmente espécies endêmicas (e.g., o peixe-borboleta Prognathodes obliquus). O Capítulo 4 aborda a ecologia do principal predador de invertebrados bentônicos na zona mesofótica do ASPSP, o verme-de-fogo Hermodice carunculata, descrevendo sua abundância e distribuição batimétrica e discutindo seu potencial em impactar as comunidades bentônicas, especialmente os corais escleractínios e os corais-negros na zona mesofótica do ASPSP. Observou-se um total de 278 indivíduos, com diferença significativa na abundância entre as zonas eufótica e mesofótica. Foi encontrada uma associação direta entre H. carunculata e 1) corais-negros (Tanacetipathes spp), 2) o coral escleractíneo Madracis decactis e 3) profundidade. Sugere-se aqui que os ecossistemas mesofóticos são essenciais para a estabilidade para as comunidades recifais eufóticas do ASPSP, tornando urgente a necessidade de novos estudos, principalmente com foco no potencial impacto da pesca e mudanças climáticas.

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.

Inshore tropical and subtropical estuaries harbor a relatively high abundance and diversity of organisms. Specifically within estuaries, mangrove and seagrass habitats provide shelter and food for a plethora of organisms, through some or all their life histories. Given the biological connection between offshore coral reefs and coastal estuaries, there is a critical need to understand the underlying processes that determine distribution and abundance patterns within mangrove-seagrass habitats. The predatory fish assemblage within the mangrove and seagrass beds of Biscayne Bay, Florida (USA), was examined over 24-hr. time periods along a distance and habitat gradient from the mangrove edge and nearshore environment (0–300 m) to farshore (301–700 m) seagrass beds. This thesis also investigated the occurrence, distribution and timing of reef fish movement between offshore coral reef habitat and inshore seagrass beds over 24-hr periods. Results indicate that fish predators differed over both the sampling period and with distance from mangrove edge. The results also demonstrated reef fishes move into Biscayne Bay at dusk and exit at dawn by utilizing Broad Creek Channel as a passageway. This work supports the idea of diel migration of selected reef fishes to inshore seagrass beds and highlights the importance of connective channels between habitats. The results suggest that the degradation or loss of seagrass habitat could differentially impact the life-history stages of reef fish species.

La métamorphose est une étape cruciale du cycle de vie de beaucoup de métazoaires. Elle est définie comme la transition d’une larve en un juvénile, souvent accompagnée de changements drastiques de morphologie, physiologie et de niche écologique. Le rôle des hormones thyroïdiennes a été mis en évidence dans la métamorphose des amphibiens, mais aussi de nombreux autres chordés comme certains poissons téléostéens ou l'amphioxus, suggérant que ce système était déjà présent et impliqué dans la métamorphose chez l'ancêtre commun de tous les chordés.Nous avons étudié le lien entre hormones thyroïdiennes et métamorphose selon deux axes. Premièrement, nous avons étudié la coordination entre la métamorphose et le recrutement larvaire, chez le chirurgien bagnard Acanthurus triostegus. Ce travail nous a permis de mieux comprendre le rôle de l’hormone thyroïdienne comme signal déclencheur d'une transition écologique importante. Dans le second axe de travail nous avons examiné l’origine de la signalisation thyroïdienne. Chez l’annélide Platynereis dumerili, nous avons identifié un récepteur fonctionnel des hormones et un rôle de l’hormone thyroïdienne dans son développement. Cela qui nous permet de démontrer que la signalisation thyroïdienne était présente à l’origine des bilateriens. Nous avons également mis en évidence un rôle des hormones thyroïdiennes dans le développement de cette espèce. Enfin dans le troisième axe nous nous sommes penchés sur l’origine de la synthèse de l’hormone thyroïdienne en retraçant l’évolution de la thyroglobuline, la protéine nécessaire à la production d’hormone chez les vertébrés. Son absence dans les autres taxons, alors que les dérivés de l’hormone y ont un rôle biologique, pose la question des mécanismes ancestraux de synthèse de ces hormones.Ces travaux explorent l’évolution de la signalisation thyroïdienne et proposent d’aborder la question du lien avec la métamorphose d’un point de vue évolutif et non-seulement développemental, afin de mieux comprendre la diversité des métamorphoses observées dans le monde animal. / Metamorphosis is a critical life step of many metazoans. It is defined as the transition between a larva and a juvenile. It comes with major changes of morphology, physiology and ecology. The role of thyroid hormone has been proven in the metamorphosis of amphibians but also in many other chordates such as teleost fishes or the amphioxus. This suggests that this system was functional and involved in the metamorphosis of the common ancestor of all chordates.We studied the link between thyroid hormones and metamorphosis according to two axes. First, we studied the coordination between metamorphosis and the larval colonization, using the convicted surgeon fish Acanthurus triostegus as a model. This work allowed us to better understand the role of thyroid hormones as a trigger signal of a major ecological transition. On the second axis, we investigated the origin of thyroid hormone signalization. In the annelid Platynereis dumerilii, we identified a functional thyroid hormone receptor and a role of TH in its development. This proves that thyroid hormone signaling was present at the basis of bilaterians. We also assessed the question of the origin of thyroid hormone synthesis by tracing back the evolution of the thyroglobulin, the protein mandatory for thyroid hormone synthesis in vertebrates. It absence in the other taxa, whereas thyroid hormone derivatives have a biological role, asks the question of the ancestral mechanisms of thyroid hormone synthesis.These works investigate the evolution of the thyroid hormone signalization and suggest to tackle the question of the link with metamorphosis from an evolutionary perspective, and not only from a developmental one, in order to better understand the diversity of metamorphosis overserved in the animal kingdom.