Data from: Biogeographic history and habitat specialisation shape floristic and phylogenetic composition across Amazonian forests

A major challenge remains to understand the relative contributions of
history, dispersal and environmental filtering to the assembly of
hyperdiverse communities across spatial scales. Here, we examine the
extent to which biogeographical history and habitat specialization have
generated turnover among and within lineages of Amazonian trees across
broad geographic and environmental gradients. We replicated standardised
tree inventories in 102 0.1-ha plots located in two distant regions - the
western Amazon and the eastern Guiana shield. Within each region, we used
a nested design to replicate plots on contrasted habitats: white-sand,
terra firme, and seasonally-flooded forests. Our plot network encompassed
26386 trees that together represented 2745 distinct taxa, which we
standardized across all plots and regions. We combined taxonomic and
phylogenetic data with detailed soil measurements and climatic data to:
(i) test whether patterns of taxonomic and phylogenetic composition are
consistent with recent or historical processes, (ii) disentangle the
relative effects of habitat, environment and geographic distance on
taxonomic and phylogenetic turnover among plots, and (iii) contrast the
proportion of habitat specialists among species from each region. We found
substantial species turnover between Peru and French Guiana, with only
8.8% of species shared across regions; genus composition remained
differentiated across habitats and regions, whereas turnover at higher
taxonomic levels (family, order) was much lower. Species turnover across
plots was explained primarily by regions but also substantially by habitat
differences and to a lesser extent by spatial distance within regions.
Conversely, the composition of higher taxonomic levels was better
explained by habitats (especially comparing white-sand forests to other
habitats) than spatial distance. White-sand forests harboured most of the
habitat specialists in both regions, with stronger habitat specialization
in Peru than in French Guiana. Our results suggest that recent
diversification events have resulted in extremely high turnover in species
and genus composition with relatively little change in the composition of
higher lineages. Our results also emphasise the contributions of rare
habitats, such as white-sand forests, to the extraordinary diversity of
the Amazon and underline their importance as conservation priorities.