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1. Assessing the response of biological communities to contrasting environmental conditions is crucial to predict the effects of global change drivers. The influence of multiple environmental factors may differ depending on the diversity facet considered, which emphasizes the need to simultaneously evaluate the functional (FD), phylogenetic (PD) and taxonomic (TD) diversity.

2. To examine how these facets of biodiversity respond to environmental changes, we studied lichen epiphytic communities across 47 beech forest fragments from two biogeographic regions. We applied structural equation modelling to relate habitat fragmentation, climate and habitat quality with FD, PD and TD. We compared the community response to contrasting climatic conditions by analysing independently Atlantic and Mediterranean communities.

3. We found different major drivers of biodiversity patterns across biogeographic regions. Habitat fragmentation performed the highest effect on lichen communities, with a reduction of FD, PD and TD at both regions. However, the influence of climate was stronger in the Atlantic region than in the Mediterranean region, where the effect of habitat quality was superior. The effect of the environmental predictors over PD and TD was both direct and indirect through the different components of FD, and their intensity and sign differed across regions. Changes in PD were not related to changes in TD.

4. Synthesis. Our results evidenced that the major environmental drivers affecting epiphytic communities were geographically structured. These drivers modified the diversity of the epiphytic community directly but also indirectly through changes in FD, which emerged as a causal but not unique determinant of PD and TD. Our findings also showed the difficulty for inferring TD through PD. These results emphasize the essential role of FD predicting part of the response of lichen communities to global change drivers but also highlight the importance of considering multiple biodiversity facets to understand the effects of environmental change on community structure.