The conservation of the biodiversity in aquatic ecosystems is one of the most important and difficult challenges in the current world. According to available information, the biodiversity of aquatic ecosystems is poorly understood in comparison with tropical terrestrial ecosystems. Thus, systematic and taxonomic analyses, the understanding of phylogenetic, biogeographical and ecological relationships represent items that need to be investigated. The first question addressed is the characterization of the ecosystem. We observed that the environmental features, mainly wideness and depth, ranges spatially along the rivers and possess the inferior zone with strong characteristics of river—lake transitional areas. The following question was to estimates fishes richness of in the Ferreira Penna Scientific Station. In order to answer this question, we used protocol techniques and obtained 130 species, of these 39 were separated by morphospecies. This fact indicates that approximately 30% of the fauna might be new or there is no available bibliography for identification. The species collected in the inventory are considered to represent a reasonable set of the ichythyofauna of the region. Lastly, we aimed to characterize fish communities and expose the patterns of distribution of species concerning the investigated habitats. As a result, we observed that the com position of species in the communities followed the substitution and addition pattern. The greatest diversity of species was observed for the final zones of the rivers. The increase in the water volume and area in some habitats of the rivers makes possible their exploitation by a larger number of individuals or new species.
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