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.