The Rufous-collared Sparrow (Zonotrichia capensis) shows phenotypic and behavioural variation throughout its continental distribution. In particular, the Patagonian subspecies Z. c. australis is strikingly distinct from other subspecies, lacking the black crown stripes that characterize the species, with a uniformly grey head or one with only subtle traces of black, and overall paler plumage. We sequenced whole genomes of 18 individuals (nine Z. c. australis and nine from other subspecies from northern Argentina) to explore the genomic basis of these colour differences and to investigate how they may have evolved. We detected a single ~465-kb divergence peak on chromosome 5 that contrasted with a background of low genomic differentiation and contains the ST5 gene. ST5 regulates RAB9A, which is required for melanosome biogenesis and melanocyte pigmentation in mammals, making it a strong candidate gene for the melanic plumage polymorphism within Z. capensis. This genomic island of differentiation may have emerged because of selection acting on allopatric populations. Concordantly, mitochondrial DNA indicated that Z. c. australis diverged from other subspecies ~400,000 years ago, probably as a consequence of Pleistocene glaciations. Phenotypic differences are consistent with Gloger’s rule, which predicts lighter coloured individuals in colder and drier climates like that of Patagonia. Future studies should focus on a contact zone in northern Patagonia where individuals show intermediate colour patterning, most likely as a result of gene flow between subspecies, to test whether colour differences are promoting the early speciation of Z. c. australis through assortative mating.

The Andean and Atlantic forests are separated by the open vegetation corridor, which acts as a geographic barrier. However, these forests experimented cycles of connection and isolation in the past which shaped the phylogeographic patterns of their biotas. We analyzed the evolutionary history of the Rufous-capped Antshrike (Thamnophilus ruficapillus), a species with a disjunct distribution in the Atlantic and Andean forests and therefore an appropriate model to study the effect of the open vegetation corridor and the Andes on the diversification of the Neotropical avifauna. We performed a phylogenetic/phylogeographic analysis including the five subspecies, using mitochondrial and nuclear genomic DNA, and also studied their differences in vocalizations and plumage coloration. Both the mitochondrial and nuclear DNA evidenced a marked phylogeographic structure with three differentiated lineages that diverged without gene flow in the Pleistocene (1.0-1.7 million years ago): one in the Atlantic Forest and two in the Andean forest. However, the two Andean lineages do not coincide with the two disjunct areas of distribution of the species in the Andes. Vocalizations were significantly different between most subspecies, but their pattern of differentiation was discordant with that of the nuclear and mitochondrial DNA. In fact, there is no song differentiation between the subspecies of the Atlantic Forest and that of the northwestern Bolivian Andes, even though they differ genetically and belong to different lineages. Consistently, no differences were found in plumage coloration between the subspecies of the Atlantic Forest and that of the southern Andes. Our results suggest a complex evolutionary history in this species, which differentiated both due to dispersion across the open vegetation corridor, likely during a period of connection between the Andean and Atlantic forests, and as a consequence of a geographic barrier in northern Bolivia. In both cases Pleistocene climatic oscillations appear to have influenced the species diversification.