Data and code from: 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 the two central clusters 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.