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, expansion of 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 to 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.
*UCE.zip - raw data and cleanreads for the UCE dataset
*ddRAD.zip - raw and demultiplexed data for the ddRAD dataset
input.zip - input files (alignments and SNP matrices) for STRUCTURE, G-PHOCS, IQ-TREE, SVDQuartets and ARLEQUIN
env.zip - raw environmental variables used to generate environmental distances, and isolation by resistance matrix generated by circuitscape used as climatic distance matrix.
*barcodes information necessary to demultiplex files can be found inside each dataset type (UCE/ddRAD) folder.