Phylogenomic analysis confirms the relationships among toucans, toucan-barbets, and New World barbets but reveals paraphyly of Selenidera toucanets and evidence for mitonuclear discordance

We reconstruct the species-level phylogenetic relationship among toucans, toucan-barbets, New World barbets using phylogenomic data to assess the monophyly and relationships at the family, generic, and specific levels. Our analyses confirmed (1) the monophyly of toucans (Aves: Ramphastidae), toucan-barbets (Aves: Semnornithidae), and New World barbets (Aves: Capitonidae) and that the toucan-barbets are sister to the toucans, an arrangement suggested, but poorly supported, in previously published phylogenies; (2) the paraphyly of lowland Selenidera toucanets with respect to Andigena mountain-toucans; and (3) evidence of some mitonuclear discordance, suggesting introgression or incomplete lineage sorting. For example, mitonuclear conflict in the phylogenetic placement of Ramphastos vitellinus subspecies suggests that Amazonian populations of Ramphastos vitellinus ariel may have introgressed mitogenomes derived from other Amazonian vitellinus taxa. To reconstruct the phylogenetic history of toucans, toucan-barbets, and New World barbets, we included all species-level taxa from the three families, with the addition of outgroups from the two major clades of Old World barbets (Megalaimidae and Lybiidae). We analyzed a combination of UCE sequences and whole mitochondrial genome sequences to reconstruct phylogenetic trees. center dot We analyzed relationships between all toucans, toucan-barbets, and New World barbets using both nuclear and mitochondrial DNA sequence data.center dot We found highly supported relationships that showed that toucan-barbets are most closely related to toucans to the exclusion of New World barbets.center dot Our results were consistent with previous research indicating that some Selenidera toucanets may be more closely related to Andigena mountain-toucans than they are to other Selenidera species.center dot We found biologically relevant discordance between phylogenetic reconstructions using nuclear and mitochondrial data that give insight into potential historical introgression within Ramphastos. Graphical Abstract Reconstruimos la relacion filogenetica a nivel de especie entre tucanes, barbudos tucanes y barbudos del Nuevo Mundo utilizando datos filogenomicos para evaluar la monofilia y las relaciones a nivel de familia, genero y especie. Nuestros analisis confirmaron (1) la monofilia de los tucanes (Aves: Ramphastidae), los barbudos tucanes (Aves: Semnornithidae) y los barbudos del Nuevo Mundo (Aves: Capitonidae), y que los barbudos tucanes son hermanos de los tucanes, un arreglo sugerido pero pobremente apoyado en filogenias publicadas anteriormente; (2) la parafilia de las tucanetas de las tierras bajas del genero Selenidera en relacion a los tucanes de montana del genero Andigena; y (3) la evidencia de alguna discordancia mitonuclear, lo que sugiere introgresion o clasificacion incompleta de linajes. Por ejemplo, el conflicto mitonuclear en la ubicacion filogenetica de las subespecies de Ramphastos vitellinus sugiere que las poblaciones amazonicas de Ramphastos vitellinus ariel pueden tener introgresion de mitogenos derivados de otros taxones vitellinus amazonicos. Para reconstruir la historia filogenetica de los tucanes, los barbudos tucanes y los barbudos del Nuevo Mundo, hemos incluido todos los taxones a nivel de especie de las tres familias, con la adicion de grupos externos de los dos clados principales de barbudos del Viejo Mundo (Megalaimidae y Lybiidae). Hemos analizado una combinacion de secuencias de elementos ultraconservados y de secuencias del genoma mitocondrial completo para reconstruir arboles filogeneticos.