Protected areas (PAs) have been created with the purpose of preserving biodiversity, acting as refuges from anthropogenic pressures. Traditionally, PAs have been designed and managed to represent mainly taxonomic diversity, ignoring other diversity facets such as its functional and phylogenetic components. Yet, functional and phylogenetic diversity are, respectively, connected with species’ roles on ecosystems and evolutionary history held within communities. Here, we focused on the amphibian, reptile, resident breeding bird, and non-flying mammal faunas of the national and natural parks of the Iberian Peninsula, to evaluate whether these PAs are adequately representing regional functional, phylogenetic, and taxonomic diversity of each group. Specifically, we computed functional and phylogenetic diversity within each PA, and then compared those values to the ones obtained from a random assembly of species from the regional pool, that was defined as the region encompassing the PA and a neighboring area of 50 km beyond its boundary. We also calculated the proportion of species in each regional pool that were present within the PAs. In general, the functional and phylogenetic diversity of amphibians, reptiles and non-flying mammals found within PAs did not differ significantly from random expectations generated from the species pertaining to the regional pool, although a few PAs showed a higher diversity. In contrast, resident breeding birds presented lower functional and phylogenetic diversity than expected by chance in many of the PAs, which could relate to climatic variables and the habitat specificity of some species. The proportion of species from the regional pools that are present in the PAs was high for amphibians, reptiles and mammals, and slightly lower for birds. These results suggest that the Iberian natural and national parks are effectively capturing the functional, phylogenetic and taxonomic diversity of most tetrapod assemblages present at the regional level. Future studies should identify priority areas to expand the representation of these biodiversity components, and assess potential effects of climate and land-use changes on current patterns.

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Evolutionary history can explain species resemblance to a large extent. Thus, if closely related species share combinations of traits that modulate their response to environmental changes, then phylogeny could predict species sensitivity to novel stressors such as increased levels of deforestation. To test this hypothesis, we used 66,949 plots (25-m-radius) of the Spanish National Forest Inventory and modelled the relationships between local (plot-level) stem density of 61 Holarctic tree species and forest canopy cover measured at local and landscape scales (concentric circles centred on the plots with radiuses of 1.6, 3.2 and 6.4 km, respectively). Then, we used the output model equations to estimate the probability of occurrence of the species as a function of forest canopy cover (i.e. response to forest loss), and quantified the phylogenetic signal in their responses using a molecular phylogeny. Most species showed a lower probability of occurrence when forest canopy cover in the plots (local scale) was low. However, the probability of occurrence of many species increased when forest canopy cover decreased across landscape scales. We detected a strong phylogenetic signal in species response to forest loss at local and small landscape (1.6 km) scales. However, phylogenetic signal was weak and non-significant at intermediate (3.2 km) and large (6.4 km) landscape scales. Our results suggest that phylogenetic information could be used to prioritize forested areas for conservation, since evolutionary history may largely determine species response to forest loss. As such, phylogenetically diverse forests might ensure contrasted responses to deforestation, and thus less abrupt reductions in the abundances of the constituent species.