Refined Phylogenomics Resolves Discordance in the Aphidinae Phylogeny

Abstract

Background/Objectives: Aphids are among the most economically damaging agricultural pests globally. However, the internal phylogeny of their largest subfamily, Aphidinae, remains contentious, particularly regarding intergeneric relationships, tribal boundaries, and monophyletic status. Here, we coupled refined taxon sampling with rigorous data-filtering strategies to resolve these persistent phylogenetic discordances. Methods: We sequenced the genomes of four aphid species: Lipaphis pseudobrassicae, Rhopalosiphum maidis, Hyalopterus arundiniformis, and Uroleucon helianthicola. Integrating these new data with public genomic and transcriptomic resources, we established a comprehensive phylogenomic framework for Aphidinae. To address conflicting topologies, we compared a taxonomically broad 157-taxa dataset against a high-completeness 47-taxa core dataset. Furthermore, we evaluated the impact of intrinsic sequence properties, such as compositional heterogeneity and substitution rates, on phylogenetic conflict. Results: Our analyses demonstrate that filtering phylogenetically inconsistent loci and accounting for site heterogeneity significantly improve the topological stability of previously recalcitrant taxa. Conclusions: This study provides a refined evolutionary framework for the Aphidinae and underscores the critical importance of rigorous data curation when resolving rapid evolutionary radiations.