Phylogenetic and functional structure of tree communities at different life stages in tropical rain forest fragments

Tropical rain forest fragmentation is considered one of the principal drivers of biodiversity loss worldwide. Fragmentation and defaunation of tropical rain forests affect the maintenance of their biodiversity in a myriad of ways. Old-growth forest plant and animal species are more likely to suffer from local extinction, not only because fragments frequently represent low quality habitats but also because of the loss of biotic interactions such as seed dispersal. In this study, we evaluated the maintenance of tree species diversity in the face of habitat fragmentation in southern Mexico using different approaches. Firstly, we used community phylogeny at different tree life stages (i.e., seeds, seedlings and adults). Secondly, we categorised plant species in different life stages into functional groups according to seed size (small seeds < 1 cm length and large seeds > 1 cm length) and, finally, by dispersal syndrome (predominantly primate dispersed). We searched for three sites of continuous forest as experimental controls where two important seed dispersers coexist, the howler (Alouatta pigra) and spider (Ateles geoffroyi) monkeys, and six forest fragments of similar sizes (ca. 3–6 ha). Three fragments were occupied only by howler monkeys, and three had no primates. We compared entire assemblages as well as assemblages of small-seeded and large-seeded species separately to determine the phylogenetic structure and patterns of species richness and the density of adult trees (> 10 cm dbh), seedlings (10–100 cm tall) and seed assemblages. Fragments and continuous forest differed in taxonomic species richness and density at all life stages when large-seeded species mainly dispersed by primates were solely considered, with numbers in unoccupied fragments being consistently lower than in continuous forests and occupied fragments. Phylogenetic clustering occurred in all habitats and for all life stages, predominantly for the seedling stage, indicating that the understory community is assembled via environmental filtering (including both biotic and abiotic processes). Habitats occupied by primates tended to present a higher phylogenetic clustering than unoccupied fragments, suggesting that primates select phylogenetically-related species in their diets and, importantly, that these foraging behaviours influence seedling recruitment patterns. The loss of taxonomic and functional biodiversity and the non-random extinction of tree species principally dispersed by primates, represents part of the evolutionary history that is being lost throughout fragmentation.