A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth’s surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.

The relative importance of contemporary and historical processes is central for understanding biodiversity patterns. While several studies show that past conditions can partly explain the current biodiversity patterns, the role of history remains elusive. We reconstructed palaeo-drainage basins under lower sea level conditions (Last Glacial Maximum) to test whether the historical connectivity between basins left an imprint on the global patterns of freshwater fish biodiversity. After controlling for contemporary and past environmental conditions, we found that palaeo-connected basins displayed greater species richness but lower levels of endemism and beta diversity than did palaeo-disconnected basins. Palaeo-connected basins exhibited shallower distance decay of compositional similarity, suggesting that palaeo-river connections favoured the exchange of fish species. Finally, we found that a longer period of palaeo-connection resulted in lower levels of beta diversity. These findings reveal the first unambiguous results of the role played by history in explaining the global contemporary patterns of biodiversity.

Using the most comprehensive fish occurrence database, we evaluated the importance of ecological and historical drivers in diversity patterns of subdrainage basins across the Amazon system. Linear models reveal the influence of climatic conditions, habitat size and sub-basin isolation on species diversity. Unexpectedly, the species richness model also highlighted a negative upriver-downriver gradient, contrary to predictions of increasing richness at more downriver locations along fluvial gradients. This reverse gradient may be linked to the history of the Amazon drainage network, which, after isolation as western and eastern basins throughout the Miocene, only began flowing eastward 1–9 million years (Ma) ago. Our results suggest that the main center of fish diversity was located westward, with fish dispersal progressing eastward after the basins were united and the Amazon River assumed its modern course toward the Atlantic. This dispersal process seems not yet achieved, suggesting a recent formation of the current Amazon system.

Although habitat fragmentation fosters extinctions, it also increases the probability of speciation by promoting and maintaining divergence among isolated populations. Here we test for the effects of two isolation factors that may reduce population dispersal within river networks as potential drivers of freshwater fish speciation: 1) the position of subdrainages along the longitudinal river gradient, and 2) the level of fragmentation within subdrainages caused by natural waterfalls. The occurrence of native freshwater fish species from 26 subdrainages of the Orinoco drainage basin (South America) was used to identify those species that presumably arose from in-situ cladogenetic speciation (i.e. neo-endemic species; two or more endemic species from the same genus) within each subdrainage. We related subdrainages fish diversity (i.e. total, endemic and neo-endemic species richness) and an index of speciation to our two isolation factors while controlling for subdrainages size and energy availability. The longitudinal position of subdrainages was unrelated to any of our diversity measures, a result potentially explained by the spatial grain we used and/or the contemporary connection between Orinoco and Amazon basins via the upstream Casiquiare region. However, we found higher neo-endemic species richness and higher speciation index values in highly fragmented subdrainages. These results suggest that habitat fragmentation generated by natural waterfalls drives cladogenetic speciation in fragmented subdrainages. More generally, our results emphasize the role of history and natural waterfalls as biogeographic barriers promoting freshwater biodiversity in river drainage basins.