Identifying the main taxonomic, phylogenetic and trait dimensions of beta diversity, and evaluating their prospective drivers, advances our understanding of patterns and processes involved in the evolution of biological assemblages. Using comprehensive databases on the distribution, phylogeny, and morphological traits (later referred as functional traits) of Amazonian freshwater fishes, we analyzed beta diversity patterns of these three dimensions to evaluate prospective historical and contemporary drivers. We mostly focused on the pure turnover components of these three beta diversity dimensions (Taxoβsim, Phyloβsim, Traitβsim) and related them to Amazon Basin-wide predictors using multiple regression on distance matrices. We found mean taxonomic beta diversity about two times higher than mean phylogenetic and six times higher than species traits beta diversity, and coincident spatial patterns in Taxoβsim and Phyloβsim dimensions, whereas Traitβsim seemed more diffuse and heterogeneous across space. Our models revealed the prominent influence of sub-basins geographic distances, habitat harshness and water color types on the taxonomic and phylogenetic dimensions of beta diversity, together with smaller individual effects of current temperature and habitat types, historical sub-basins connections and marine incursions, and sampling effort. By contrast, Traitβsim was weakly explained only by sampling effort and current sub-basins hydro-morphological conditions. These results point to leading effects of dispersal limitation, environmental filtering and historical contingencies in explaining Amazonian fish assemblages taxonomic and phylogenetic beta diversity patterns, but not functional traits turnover.

Reconciling niche-based process and neutral dynamics in a portion of an infinite system, the regional species pool may be already not free parameter, and the divergent ecological-evolutionary mechanisms may operate consistently. The individual-based model was implemented in the two-dimensional grid with periodic boundary condition. The model was explored using a fixed speciation rate, and a range of system sizes, dispersal rates, environmental structures and initial conditions of regional species pool. The model communities in the center of system had a fixed population size, and approximated from an area encompassing independent biogeographic units to an area packed in a biogeographic unit with open boundary conditions, and presented the three environmental structures; four humps, linear and random. Across scenarios, the number of guilds in system achieved first to a stationary state; then, the species richness converged eventually to a dynamical equilibrium through speciation-extinction balance. In simulations, the per capita ecological difference among species only contributed to the probabilities of immigration success, so the weighted lottery process was more efficient and immediate at higher dispersal rates. The increase of functional redundancy in model communities suggested that the relative role of neutral dynamics increased in an area encompassing independent biogeographic units. The variation partitioning based on canonical analysis inferred that not only the neutral dynamics among the species of single guild, but also the competition-colonization trade-off among the species of more than two guilds with similar environmental optimum and different levels of specialization operated in the spatial structures found within and among patchy habitats. Ecologist to disentangle the influence of alternative processes must shift focus from the contribution of local competitions and regional dispersals to detecting the spatio-temporal-environmental scales on which the per capita ecological difference and equivalence among species are emerged through divergent ecological-evolutionary mechanisms.