Species level phylogenomics of New World toucans and barbets: a test of generic monophyly and higher-level relationships in a model Neotropical bird clade

We reconstruct the species level phylogenetic relationship among New World toucan and barbet taxa using phylogenomic data to test monophyly and relationships among the genera. This study includes all species level taxa from three relevant families, the toucans (Aves: Ramphastidae), the New World barbets (Aves: Capitonidae), toucan-barbets (Aves: Semnornithidae), and outgroups from the two major clades of Old World barbets (Megalaimidae and Lybiidae). We analyzed a combination of UCE sequences and their flanking regions and whole mitochondrial genome sequences to reconstruct phylogenetic trees. Our analyses confirmed (1) the monophyly of each family and that toucan barbets (Semnornithidae) are sister to the toucans (Ramphastidae), an arrangement suggested, but poorly supported in previously published phylogenies, (2) the potential paraphyly of lowland Selenidera toucanets with respect to Andigena mountain-toucans, and (3) the lack of monophyly of montane toucan genera as hypothesized by Haffer (1974). Furthermore, conflict in the placement of Ramphastos vitellinus subspecies between mtDNA genome and nuclear UCE sequence phylogenetic reconstructions suggests that Amazonian populations of Ramphastos vitellinus ariel may have introgressed mitogenomes derived from other Amazonian vitellinus taxa, while being historically connected to R. v. ariel populations in the Atlantic Forest.