CaveBatDiversity_Brazil: Data and code for a national-scale assessment of taxonomic, phylogenetic, and functional diversity of cave-associated bats in Brazil

This dataset accompanies the manuscript "Multidimensional diversity assessment of cave-associated bats in Brazil reveals major conservation gaps" and contains all spatial, tabular, and script files required to reproduce all analyses and figures. Cave-associated bats occupy ecologically specialized niches and are among the most vulnerable bat guilds, yet large-scale assessments of their multidimensional diversity remain scarce. This study provides the first national-scale integration of taxonomic (TD), phylogenetic (PD), and functional diversity (FD) for cave-associated bats across Brazil, using expert species range maps, trait-based metrics, and molecular phylogeny within a standardized 10 km × 10 km grid (n = 72,180 cells). Diversity estimates were assessed across multiple percentage thresholds at both national and biome-specific scales, and spatially overlapped with land-use pressures (agriculture, mining, urban expansion) and protected area coverage. REPOSITORY STRUCTURE: Perea et al. 2026. BiodivConserv_data.zip — Supporting data files, including the master spatial dataframe with all computed diversity metrics and overlap variables (Perea et al. 2026. BiodivConserv_final_df_diversities2_updated_revision3.rds), the molecular phylogenetic tree (Perea et al. 2026. BiodivConserv_Brazilian_cave_bat_phylogeny_DCS_20.11.2023.TRE), and the functional trait databases (Perea et al. 2026. BiodivConserv_Cave Associated Trait dataset.csv). Perea et al. 2026. BiodivConserv_shapefiles.zip — All shapefiles used in the spatial analyses, including layers for Brazilian biomes, caves, species ranges, land-use change, and protected areas. Biome boundaries, protected areas, and land-use change layers were obtained from the publicly available MapBiomas platform (https://brasil.mapbiomas.org/en/). Perea et al. 2026. BiodivConserv Analyses.R — Main R script for building the 10 km grid, computing TD (species richness), PD (Faith's PD, PSV, MNTD), and FD (FRic, FDis, FEve, FDiv) per grid cell, and applying national-scale percentage thresholds. Produces final_df_diversities2. Perea et al. 2026. BiodivConserv Annotated Summaries.R — Annotated R script for national-scale analyses: applies national diversity thresholds, assigns biomes to grid cells, and generates summary tables and maps of top-diversity cell overlap with protected areas and land-use pressures. Perea et al. 2026. BiodivConserv Annotated Figures.R — Annotated R script for biome-scale analyses: computes biome-specific diversity thresholds, identifies top-diversity cells within each biome, and generates summary tables of overlap with protected areas and land-use pressures. NOTE: Reviewers must update the setwd() path in each R script to their local directory before running the code.