Data from: Phylogeny, traits and biodiversity of a neotropical bat assemblage: close relatives show similar responses to local deforestation

If species' evolutionary pasts predetermine their responses to evolutionarily novel stressors, then phylogeny could predict species survival in an increasingly human-dominated world. To understand the role of phylogenetic relatedness in structuring responses to rapid environmental change, we focused on assemblages of Neotropical bats, an ecologically diverse and functionally important group. We examined how taxonomic and phylogenetic diversity shift between tropical forest and farmland. We then explored the importance of evolutionary history by ascertaining whether close relatives share similar responses to environmental change and which species traits might mediate these trends. We analyzed a 5-year data set (5,011 captures) from 18 sites in a countryside landscape in southern Costa Rica using statistical models that account and correct for imperfect detection of species across sites, spatial autocorrelation, and consideration of spatial scale. Taxonomic and phylogenetic diversity decreased with deforestation, and assemblages became more phylogenetically clustered. Species' responses to deforestation were strongly phylogenetically correlated. Body mass and absolute wing loading explained a substantial portion of species variation in species' habitat preferences, likely related to these traits' influence on maneuverability in cluttered forest environments. Our findings highlight the role that evolutionary history plays in determining which species will survive human impacts and the need to consider diversity metrics, evolutionary history, and traits together when making predictions about species persistence for conservation or ecosystem functioning.Array of Costa Rican bat capture dataCapture data collected from the field and arranged in an R data array. Array includes: (1) the capture array (X), with the site, year, visit and species information; (2) matrix of the number of visits conducted at each site by year combination (nrep); (3) the pairwise distance between sites (D); (4) scaled and centered proportion of area covered by trees across all spatial scales; see full model explanation (Env); (5) relative elevation of site compared to surroundings (terrain); (6) whether or not the site was a coffee field (coffee.dummy)array.rdataFull occupancy model with traitsR and JAGS code for the full phylogenetic occupancy model with influence of traits includedmodel_with_trait_for_supplement.RFull occupancy model without traitsR and JAGS code for the full occupancy model not including traits as an explanatory variablemodel_notrait_for_supplement.