Phylogenetic patterns of rarity and vulnerability in the flora of a temperate mountain range

Species rarity has puzzled ecologists for decades owing to its theoretical fundamentals and practical implications. The main concern that rarity raises from a conservation standpoint is that rare species tend to have higher extinction risk. Understanding the underlying phylogenetic patterns of rarity can shed light on the evolutionary processes yielding rarity, contribute to forecasting potential vulnerable species or lineages, and assess the consequences of the loss of rare species. Here, we apply Rabinowitz's rarity classification scheme and explore phylogenetic patterns in the flora of the Pyrenees, a temperate mountain range. We first categorized species according to their geographic range (endemicity and regional geographic range), habitat specialization and local abundance. Then we analyzed the phylogenetic signal of each rarity type, along with the phylogenetic association between species according to their rarity, and decomposed the variation of rarity among taxonomic levels to better understand its diversification through time. Finally, we estimated the expected loss of phylogenetic diversity (PD) in the regional flora if rare species go extinct. All rarity types showed a certain degree of phylogenetic signal, with endemics, species of limited regional geographic range and habitat specialists forming groups of phylogenetically close species. The decomposition of variation supported these results, as the rarity types with the strongest signal had more variation explained by higher taxonomic levels. The loss of these groups of species had different consequences based on the type of rarity, with the disappearance of habitat specialists having the strongest, negative effect on PD. Our results show a general pattern of phylogenetic association in rarity among the flora of the Pyrenees, which leads to increased vulnerability along certain branches of the Tree of Life. Phylogenetic patterns should be taken into account in conservation planning to effectively protect all facets of biodiversity