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Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modeling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380-166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.

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Aim Continental evolutionary radiations provide opportunities to understand how landscape evolution and biotic factors interact to generate species diversity. Additionally, understanding whether diversification dynamics differ between montane and lowland environments is a long‐standing question with few comparative analyses in the Neotropics. To address these questions, we investigated the biogeographical patterns and the evolutionary processes underlying the diversification of a songbird genus, and compared diversification dynamics of clades occurring in lowland and montane Neotropical habitats. Location Neotropical montane and lowland forests. Taxon Arremon(Aves: Passerellidae). Methods We sequenced genomic data (ultra‐conserved elements, UCEs) of 92 individuals (including historical skin specimens) comprising 47 of 50 currently recognized subspecies in the genus and collected habitat association data to (1) build the most complete phylogenetic hypothesis for the genus to date using maximum likelihood and Bayesian methods with a concatenated matrix, and a multi‐species coalescent method based on quartets; and (2) reconstruct the evolution of their ancestral ranges, habitat association and diversification rates. Results All phylogenetic methods recovered essentially the same topology with strong support values for most interspecific nodes revealing relationships among species. We found evidence for a montane and humid ancestral range in Central America in the late Miocene and a later expansion into the lowlands of Central America, as well as into the lowlands and mountains of South America. Despite some temporal variation in diversification rate, we found overall similar diversification dynamics between montane and lowland clades. Main conclusion Species diversity within the genus is likely underestimated by the current taxonomic arrangement. The colonization of lowlands and dry forests, and expansion across South America, may have provided new geographical and ecological opportunities for speciation resulting in high species diversification. Overall diversification dynamics were comparable between montane and lowland clades, contrasting with previous studies focused on such comparisons for Neotropical birds.