Matrix-protection rather than protected area conservation can safeguard multilevel amphibian diversity in Colombian agroforestry systems

Land use change and intensification are among the major threats to amphibian diversity. Nonetheless, human-modified agroforestry systems have been shown to preserve significant amphibian species richness, presumably because they provide alternative microhabitat structures that can be used by several species. Few studies have systematically analyzed the response of amphibians to different management types within these agroforestry systems considering multiple components of diversity. We assessed the composition of amphibians and their taxonomic, functional, and phylogenetic diversity across an agroforestry management gradient in the northern Andes, Colombia. This nonlinear gradient included montane and riparian forests and 6 different land-use systems. We evaluated amphibian assemblages along 34 independent transects covering the entire gradient and applying standardized visual and acoustic encounter techniques. We recorded 18 ecosystem structure variables to characterize the different management systems. We recorded a total of 3796 individuals belonging to 14 species and 7 families during 320 hours of transect sampling. Agroforestry systems with shaded plantations showed the highest overall amphibian species richness, while functional and phylogenetic diversity was highest in wetlands and a riparian forest fragment. Cattle pastures, the most intensive management type showed functional and phylogenetic homogenization and the lowest species richness. Structural habitat parameters that best explained the change in species composition were related to vegetation coverage and density. Our results highlight that total amphibian diversity cannot be preserved within a single management type. While less intensive agroforestry systems could be a helpful alternative for amphibian conservation in managed landscapes, linking natural forest fragments and sustainable agroforestry systems in a mosaic matrix design are key to maintaining diversity outside and inside of protected areas. • Matrix conservation can protect multilevel amphibian diversity in the Colombian Andes. • Intensive land-use leads to functional and phylogenetic homogenization. • Shaded agroforestry plantations show high levels of amphibian biodiversity. • Maintaining a heterogeneous matrix is the key to preserving diversity in managed landscapes. • Effective conservation outside protected areas requires an integrated approach.