Diversification in Amazonian Hypocnemis antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs)

Warbling antbirds consist of an avian genus (Hypocnemis) with a wide distribution, confined to the Amazon basin, and whose true diversity and evolutionary history remain poorly understood. Here, we used sequences of 2,222 Ultra-conserved Elements (UCEs) and 30 exons loci from 58 specimens belonging to all currently recognized Hypocnemis species and all but one subspecies to infer phylogenies, population structure, interspecific limits, and the genus' biogeographic history. A consensus of phylogenies, networks, and phylogeographic structure analyses recovered up to thirteen independent evolutionary units within the genus, which currently has eight named species. Except for one case, these lineages corroborate currently recognized taxa; based on our analyses, we propose the recognition of two additional species in the genus: H. implicata and H. ochraceiventris. From a biogeographic perspective, our estimated scenarios indicate separation of the two main Hypocnemis lineages during the Miocene, subsequent concentration of Pliocene splits in western and northern Amazonia, and more recent Pleistocene diversification in the southeastern part of the basin. Lineage relationships in the southeastern group are complex, and support a pattern whereby lineages in close contact on the Brazilian shield are not each other's closest relatives. This pattern challenges simplistic biogeographic interpretations and suggests that independent range-expansion and admixture events, local extinction, and even behavioral attributes under strong divergent selection, may be coupled with vicariant scenarios.