Dispersal, isolation and local adaptation promote speciation in South American savannas as indicated by a phylogenomic analysis of a passerine

South American savannas are a disjunct biome with an unclear evolutionary history. We tested hypotheses about their Quaternary history and evolution of savanna cores through fragmentation or dispersal from the Cerrado. We used genomic data (genotyping-by-sequencing) and ecological niche models of the Burnished-buff Tanager (Stilpnia cayana Linnaeus 1766) to evaluate intraspecific differentiation, gene flow, past range shifts, and landscape-genomics association. We found clear genomic differences between populations on each side of the Amazon basin and high admixture in the Marajó Island and Bolivia. Landscape genomics analysis indicated that the Amazon River, isolation by distance and temperature predict genomic differentiation in this bird. Taken together, the results suggest that a combination of dispersal from the Cerrado, isolation due to geographic distance and the Amazon River basin, and local adaptation shaped the species diversification. We propose that the populations on each side of the Amazon River be considered distinct species (S. cayana at the north and S. flava at the south) with subspecies huberi representing part of a hybrid zone between them, located on Marajó island at the mouth of the river.