Genomic phylogeography of the white Crowned Manakin (aves: Pipridae) illuminates cryptic differentiation and extreme song evolution

The complex history of the Neotropics has generated patterns of isolation that make this region among the most species-rich in the world, with a great number of cryptic taxa yet to be discovered. Detailed phylogeographic studies are needed to uncover this cryptic diversity. Further, such studies undertaken at the continental scale have the potential to reveal the hidden story of a species’ history. The White-Crowned manakin (Dixiphia pipra), is a small (8.5-11.8cm) passerine bird, which is broadly distributed across the Amazon basin, with additional populations in the Brazilian Atlantic Forest and Central America. Dixiphia spans every known type of biogeographic barrier in South America (e.g. the Andes, major Amazon rivers, etc) but is generally restricted to tropical rainforest. We studied this species complex using a reduced representation genomic sequencing technique (ddRAD), to sample thousands of loci from ~250 individuals across most of the known range. Our analyses imply a new hypotheses of species delimitation for the group, with at least 5-7 reciprocally monophyletic, deeply diverged lineages. We infer a well-supported phylogeny which broadly recapitulates variation in song and Amazonian areas of endemism. Broadly, we identify a Central American clade, highland and lowland Peruvian clades, a Guyana shield clade, southern Amazonian clades, and an Atlantic forest clade.