DNA ambiental metabarcoding aplicado ao manejo e conservação de peixes

Abstract

The Neotropical region comprises one of the greatest diversity of freshwater fish in the world. However, this biodiversity faces unprecedented levels of anthropic impacts. Thus, the assessment of biodiversity is pivotal for defining the most appropriate management and conservation strategies. This assessment depends on reliable detection and accurate identification of species, thus, additional methods, associated with traditional taxonomic identification, are being increasingly implemented worldwide, as environmental DNA metabarcoding. However, despite the exponential increase in eDNA metabarcoding publications, most studies have been conducted in temperate regions and in reasonably accessible areas, and few studies are conducted in megadiverse regions, such as the Neotropics, especially in regions affected by damming, one of the major stressors for the freshwater fish community. Currently, the understanding of how eDNA metabarcoding can be a well-established method for biodiversity assessment and ecological monitoring in reservoirs is relatively limited and methodological aspects such as lack of knowledge of local biodiversity and absence of sequences in the reference database, biases of primer and the different forms of taxonomic identification (MOTUs x ASVs) need to be better evaluated and understood before applying this technique in large-scale fish community identification. In this thesis, we developed a set of mini-barcodes primers, based on a customized reference database. Moreover, we validated this set of molecular markers in different mock communities and finally, we applied the eDNA metabarcoding methodology in a Neotropical reservoir, comparing the results obtained with data from gillnets, representing traditional fishing methods. Collectively, the results of this thesis highlight the importance of a customized reference database for the correct and reliable identification of species. Furthermore, our results demonstrated the complementary role of eDNA metabarcoding in fish monitoring.