Data and code for a manuscript on bat diversity and conservation in Brazil.

Data and code for a manuscript on bat diversity and conservation in Brazil. ABSTRACT Aim: Cave-associated bats share unique ecological traits and are often highly vulnerable, yet their diversity patterns remain poorly understood across large spatial scales. Despite increasing anthropogenic pressures on subterranean habitats, there has been no large national-scale assessment integrating taxonomic (TD), phylogenetic (PD), and functional diversity (FD) for these species in Brazil, a continental-scale country with pressing conservation issues. Here, we: (1) mapped and compared TD, PD, and FD of all known cave-associated bats across major terrestrial Brazilian biomes; (2) assessed the impacts of land-use change and their spatial overlap; and (3) evaluated the effectiveness of the protected area network. Location: Brazil, encompassing all major terrestrial biomes: Amazon, Atlantic Forest, Caatinga, Cerrado, Pantanal, and Pampa. Methods: Using range maps for cave-associated bat species, we calculated TD, PD, and FD within 10 km × 10 km grid cells (n = 72,180). FD was quantified using trait-based metrics and PD estimated using a pruned molecular phylogeny. We identified spatial hotspots for each diversity facet, evaluated their congruence, and assessed overlap with anthropogenic pressures (e.g., deforestation, agriculture, mining) and the national protected area network. DATASET This Zenodo contains the CaveBatDiversity_Brazil dataset, which includes all spatial, tabular, and script files used in the analyses. The folder is organized into several subfolders with shapefiles for biomes, Brazil land use change, caves, protected areas, and species ranges. A Data subfolder provides additional files needed for calculating different dimensions of diversity. These include two CSV files with trait information (Brazilian trait categories.csv and Brazilian traits.csv) used to calculate functional diversity, as well as a phylogenetic tree file (Brazilian cave bat phylogeny.TRE) used to calculate phylogenetic diversity. Within the coding workflow, the final dataframe is referred to as final_df_diversities2. This file was built step by step, with new columns added as different diversity metrics and top-cell overlaps were calculated. The completed dataframe contains all results used in the analyses, including the overlap variables. Further details on the meaning of these overlap variables are provided in the accompanying code. A Code subfolder contains two R scripts: one for performing the diversity calculations and another for generating the visualizations.