This study examines the evolutionary relationships and phylogeographic patterns of the genus Gymnopithys (Ayes: Thamnophilidae). Phylogenetic reconstructions were used to evaluate the monophyly of Gymnopithys, to assess phylogeographic relationships, and to estimate the divergence times and historical demography of Gymnopithys lineages.

Phylogenetic analyses using six mitochondrial and three nuclear markers found Gymnopithys species to cluster in two clades ( lunulatus-salvini; and bicolor-leucaspisrufigula) that were closely related to Rhegmatorhina. The results did not show support for the paraphyly of Gymnopithys as previously suggested. The ultrametric tree shows that the events that originated those three lineages happened rapidly, which make it difficult to resolve. No significant genetic structure was found within Gymnopithys species, which question about the validity of ten of the recognized subspecies.

The Amazonian Gymnopithys-Rhegmatorhina clade originated during the Early Pliocene. In the lunulatus-salvini clade, a western Amazonia north/south split at the Late Pliocene is concurring with the uplift of the Fitzcarrald Arch, an event that caused the edaphic conditions that allowed the formation of isolated endemic terra-firme forests in Western Amazonia. In the bicolor-leucaspis-rufigula clade, an initial northern Amazonia west/east split at the Early Pleistocene was followed by dispersal out of Amazonia, and subsequent colonization to Choco and Central America with further differentiation of bicolor. The timing of the Amazonian split is coincident with a scenario of major Amazon Basin drainage reorganization. The timing for the differentiation of the trans-Andean bicolor suggests dispersal of the ancestral lineage across the Andes. The results also uncovered the existence of asymmetrical introgression between leucaspis and rufigula, that probably took place at the upper and lower Rio Negro. The biogeographic origins of each of the five species currently included in Gymnopithys reveal that the historical diversification of the Neotropical lowlands is complex and affected by multiple events, such as vicariance, dispersal and introgression.