The goal of this research was to determine the relative quality of near shore marine areas by investigating their influence on Haemulidae community structure, distribution pattern, condition, and growth. Habitat was defined at the small spatial scale of individual habitat types such as seagrass beds, mangroves and coral reefs, and at the broader spatial scale of the interconnection of these individual habitat types within a mosaic (IHM). Ten spatial, biotic and abiotic parameters (percentage coverage of sand, mangroves, hard substrate, and seagrass, turbidity, pH, salinity, temperature, average depth, and predator density) were investigated. These environmental characteristics acted as proxies for the quality of IHMs. The major findings of the research were: (1) IHMs and discrete habitat types in tropical marine systems are not always equal in quality. Further, the highest quality IHMs/discrete habitat types have the critical resources whether spatial, abiotic or biotic, at the optimum levels needed by organisms to carry out their critical life functions; (2) IHMs of the highest quality contain all the discrete habitat types needed by organisms to carry out their life processes in a spatial arrangement that maximizes energy savings; (3) IHMs can be of high quality in the absence of one habitat type, if this habitat type is replaced by another that can take on its ecological role; and (4) the percentage cover of hard substratum and seagrass, temperature, and predator density have a big impact on Haemulidae distribution pattern, community structure, condition and growth. In addition, this research highlighted some of many characteristics of benthic habitats such as type and configuration that should be included in the design of Marine Protected Areas for the effective management of fisheries resources. Effective Marine Protected Areas should have (1) large overall area with benthic habitat types of high quality; (2) spatial configurations with short distances (corridors) between habitat types; (3) spatial arrangements that place all individual habitat types in connection with all other habitat types so that energy expenditure in moving among habitat types is reduced; (4) habitats with high structural complexity; and (5) the inclusion of all the habitat types needed by focal organisms to carry out their life processes, or surrogate habitat types that can take on the role of ones that are absent.

Les transitions terrestre-aquatique jouent un rôle primordial dans le fonctionnement des écosystèmes. Dans les cours d'eau qui cessent de s'écouler périodiquement, ces transitions se développent latéralement au travers des zones ripariennes mais aussi longitudinalement le long du lit du cours d'eau. L'objectif de ce travail de thèse était de déterminer les effets de ces transitions terrestre-aquatique dans les lits des cours d'eau sur les communautés d'invertébrés terrestres et sur dynamique de la matière organique particulaire, un processus écologique fondamental au fonctionnement des cours d'eau. Les résultats montrent que communautés d'invertébrés ripariens sont peu dépendantes des ressources aquatiques du cours d'eau mais sont essentielles au maintien de la diversité en invertébrés dans les lits asséchés. La matière organique est transportée et se décompose par à coup lors des conditions aquatiques, influençant potentiellement la disponibilité en nutriments dans les réseaux hydrographiques / Aquatic-terrestrial transitions play a major role in the functioning of ecosystems. In rivers that periodically cease to flow, these transitions move laterally in riparian zones and longitudinally along dry riverbeds. The objective of this thesis was to determine in drying rivers the effects of aquatic-terrestrial transitions on terrestrial invertebrate communities and on particulate organic matter dynamic, a key ecological process for ecosystem functioning. The results show that riparian communities are poorly dependent on aquatic resources from the rivers but are essential to invertebrate diversity in dry riverbeds. Organic matter has a pulsed dynamic in drying rivers with transport and processing stages limited to aquatic conditions, potentially influencing nutrient availability in river networks