Lineage divergence following hybridization in the Black-cheeked Gnateater, an Atlantic Forest endemic bird

Reticulate evolution through introgressive hybridization can lead to diverse outcomes, yet its long-term role in lineage divergence remains unclear. We investigate the evolutionary history of the Black-cheeked Gnateater (Conopophaga melanops), an Atlantic Forest endemic bird that shows marked geographic variation in plumage. The central subspecies, C. m. perspicillata, exhibits 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 and phenotypic data, we assessed genetic structure and trait variation across the species range. Our analyses reveal four population genetic clusters, with the two central clusters exhibiting clear signatures of admixed ancestry. Despite admixture, central populations are genetically differentiated from both northern and southern lineages and sing a distinct, slower-paced song outside the acoustic space of either, consistent with transgressive traits or divergence following admixture. We propose that hybridization followed by climate-driven geographic isolation in forest refugia contributed to the formation of a divergent, reticulate lineage within the Black-cheeked Gnateater, offering an opportunity to investigate how gene flow and allopatric divergence interact to shape lineage diversity and providing a natural framework for testing the conditions under which reticulate lineages may emerge, persist, and diverge.