Aim Disentangling the effects of climate and historical factors on biodiversity distribution remains a challenge for biogeographers. Here, we provide an analytical framework to discriminate the contributions of contemporary climate and the biogeographical history of taxa to the geographical distributions of phylogenetic lineages. Furthermore, we evaluate the constraint that the biogeographical history of clades exerts on the association between climate and clade distribution, i.e. the historical legacy of climatic effects. As a case study, we analysed the distributions of amphibian lineages across the Americas. Location The Americas. Methods We tallied the number of amphibian species per genus in each of 262 ecoregions. Each ecoregion was described by the composition of phylogenetic lineages using phylogenetic fuzzy weighting. The composition of amphibian genera and phylogenetic clades represented the distributions of shallow and deep phylogenetic nodes, respectively. We characterized each ecoregion by the biogeographical history of amphibian taxa and its current climate, whose influences on shallow and deep phylogenetic nodes were analysed using variation partitioning analysis. Results The association between climate and the distributions of deep phylogenetic nodes showed a strong historical legacy, although the distribution of amphibian genera was mostly associated with climate. Hyloidea were associated with a Gondwanan origin and higher annual mean temperatures, whereas other clades (e.g. Caudata) were related to a Laurasian origin and higher temperature seasonality. Microhylidae were related to occurrence in the Early Jurassic in Gondwana and recent occurrence in the Neotropics. Main conclusions Biogeographical patterns can be thought of as the net outcome of evolutionary, historical and ecological processes. Although temperature is likely to affect the ecology of amphibians, the effects of climate on the distributions of deep phylogenetic nodes were strongly constrained by the biogeographical history of clades. Nevertheless, local, climatically driven processes are likely to influence the distributions of shallow phylogenetic nodes. The historical biogeography of clades might help to explain the interplay between evolutionary and environmental processes in determining assembly patterns found elsewhere.

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BackgroundWe evaluated the direct and indirect influence of climate, land use, phylogenetic structure, species richness and endemism on the distribution of New World threatened amphibians.Methodology/Principal FindingsWe used the WWF’s New World ecoregions, the WWFs amphibian distributional data and the IUCN Red List Categories to obtain the number of threatened species per ecoregion. We analyzed three different scenarios urgent, moderate, and the most inclusive scenario. Using path analysis we evaluated the direct and indirect effects of climate, type of land use, phylogenetic structure, richness and endemism on the number of threatened amphibians in New World ecoregions. In all scenarios we found strong support for direct influences of endemism, the cover of villages and species richness on the number of threatened species in each ecoregion. The proportion of wild area had indirect effects in the moderate and the most inclusive scenario. Phylogenetic composition was important in determining the species richness and endemism in each ecoregion. Climate variables had complex and indirect effects on the number of threatened species.Conclusion/SignificanceLand use has a more direct influence than climate in determining the distribution of New World threatened amphibians. Independently of the scenario analyzed, the main variables influencing the distribution of threatened amphibians were consistent, with endemism having the largest magnitude path coefficient. The importance of phylogenetic composition could indicate that some clades may be more threatened than others, and their presence increases the number of threatened species. Our results highlight the importance of man-made land transformation, which is a local variable, as a critical factor underlying the distribution of threatened amphibians at a biogeographic scale.