Geographic isolation after admixture generates a distinct lineage in an Atlantic Forest bird

Although traditionally viewed as opposing divergence, hybridization can have diverse evolutionary outcomes. Yet, its role in lineage divergence remains unclear. To investigate this process, we examined the evolutionary history of the Black-cheeked Gnateater (Conopophaga melanops) from the Atlantic Forest of eastern Brazil. The central subspecies, C. m. perspicillata, exhibits plumage traits intermediate to northern and southern populations, raising the question of whether this pattern reflects isolation-by-distance, recent hybridization, or past admixture. Using genome-wide markers from sequencing of ultraconserved elements along with phenotypic data, we assessed genetic structure and trait variation across the species' range. Our analyses reveal four population genetic clusters, with central populations exhibiting clear signatures of historical admixture. Despite this admixture, central populations are genetically differentiated from northern and southern lineages and sing a distinct song, suggesting divergence following admixture or transgressive segregation. We propose that past hybridization followed by geographic isolation contributed to the formation of a divergent, reticulate lineage within the Black-cheeked Gnateater. This system provides an opportunity to investigate how gene flow and allopatric divergence interact to shape lineage diversity and offers a natural framework for testing the conditions under which reticulate lineages may emerge, persist, and diverge.