Phylogenomics reveals the timescale of diversification in Amblycera

Recently, genomic approaches have helped to resolve phylogenetic questions in many groups of parasitic organisms, including lice (Phthiraptera). However, these approaches have still not been applied to one of the most diverse groups of lice, Amblycera. To fill this gap, we applied phylogenomic methods based on genome-level exon sequence data to resolve the relationships within and among the families of Amblycera. Our phylogenomic trees support the monophyly of the families Ricinidae and Laemobothriidae. However, the families Trimenoponidae and Gyropidae are not monophyletic, indicating that they should be merged into a single family. The placement of Trinoton is unstable with respect to Boopiidae and Menoponidae, and we suggest recognizing Trinotonidae as a separate family. At the genus level, the genera Colpocephalum, Hohorstiella, Menacanthus and Ricinus were recovered as paraphyletic. Regarding generic complexes, the tree revealed the Menacanthus complex to be monophyletic, but the Colpocephalum complex paraphyletic, including genera not traditionally placed in this group. Dating analysis suggests that the divergence among families of Amblycera occurred shortly after the Cretaceous–Paleogene boundary 66 Mya. Cophylogenetic analyses revealed many host-switching events during the diversification of Amblycera, indicating that the evolutionary history of Amblycera does not tightly mirror that of its hosts. Ancestral host reconstructions revealed that the ancestral host of Amblycera was most likely a bird, with two host switching events to mammals. By combining phylogenomics, molecular dating and cophylogenetic analyses, we provide the first large-scale picture of amblyceran evolution, which will serve as a basis for future studies of this group.