Different processes will influence and regulate the composition and species diversity in a community, including climate, evolutionary history, environmental heterogeneity, barriers to dispersion, and anthropogenic disturbance on natural habitats. This influence can result in current ecological patterns that might increase or decrease biodiversity, particularly considering the distribution of biological communities in environmental gradients. In this thesis, i will investigate many important processes acting in the structuring of species richness, functional diversity, phylogenetic diversity, taxonomic endemism, and phylogenetic endemism of neotropical bats. The thesis is divided into four chapters, and I will present the first two in this document. In the first chapter, "Historical climate reveals adaptive and evolutionary characteristics of bats from the Neotropical savanna, we evaluated the relative contribution of ecological factors (vegetation and climate) and geologic and climatic history on the structuring of bat communities in the Cerrado, and how these characteristics influence current patterns of species richness, functional and phylogenetic diversity. In the second chapter, "Flying over Amazon waters: the role of rivers in the distribution patterns and endemism of neotropical bats", our main objective was to understand the patterns of beta diversity and endemism of bats in cis- Andean Amazonia and their relationships with the large fluvial systems of the Amazon. The main aim of the third chapter is to identify the possible impacts of landscape changes on the biogeographic patterns of phylobetadiversity and to infer the different patterns of endemism of the bat communities in the Cerrado, under a neo- and paleo-endemism perspective. Finally, the aim of the fourth chapter is to investigate the ecological processes that determine community assembly in the Cerrado-Mata Atlântica ecotone region in comparison to the central regions of both biomes, using mathematical models based on evolutionary history and functional traits of the species.