Reconstruction of the aphid phylogeny inferred from low-coverage genomes

Aphids (Hemiptera: Aphididae) are a lineage of ~5200 plant-feeding insects most abundant in temperate regions. The diversification of aphids is thought to be a rapid radiation, whereas abiotic and biotic factors heavily influence the morphologies. These factors have clouded the taxonomy at all taxonomic ranks, and the effect can be viewed in many incongruent molecular and morphological phylogenies. In this study, we address this problem using both low-coverage genome and transcriptome data to estimate the phylogenomic relationships between 17 subfamilies, and 21 tribes, with 81 taxa. We predicted a novel well-curated dataset of orthologues that included 2545 genes to estimate a concatenated maximum likelihood and multi-species coalescent species trees. Our results suggest that there are four main clades of Aphididae subfamilies, which is a novel finding when compared to previous Sanger sequencing-based phylogenetic studies and recent phylogenomic studies. Furthermore, we found additional discrepancies between taxonomy and phylogeny. This research provides additional support for many of the relationships between the Aphididae subfamilies while confirming that other data may be needed to resolve short branches along the backbone.