Refined Phylogenomics Resolves Discordance in the Aphidinae Phylogeny

Area of Science:

• * Entomology
• * Phylogenomics
• * Evolutionary Biology

Background:

• * Aphids (Aphidinae) are major agricultural pests, causing significant economic damage worldwide.
• * The internal phylogeny of the Aphidinae subfamily is poorly understood, with ongoing debates about intergeneric relationships, tribal classifications, and monophyly.
• * Previous phylogenetic studies have been hampered by data inconsistencies and conflicting topologies.

Purpose of the Study:

• * To resolve persistent phylogenetic discordances within the Aphidinae subfamily.
• * To establish a robust phylogenomic framework for understanding aphid evolution.
• * To investigate the impact of data quality and filtering strategies on phylogenetic accuracy.

Main Methods:

• * Sequencing of four new aphid genomes: *Lipaphis pseudobrassicae*, *Rhopalosiphum maidis*, *Hyalopterus arundiniformis*, and *Uroleucon helianthicola*.
• * Integration of new genomic data with existing public genomic and transcriptomic resources to build a comprehensive phylogenomic dataset.
• * Comparison of a broad 157-taxa dataset with a high-completeness 47-taxa core dataset to assess phylogenetic stability.
• * Evaluation of sequence properties like compositional heterogeneity and substitution rates to identify sources of phylogenetic conflict.

Main Results:

• * Filtering phylogenetically inconsistent genetic loci significantly enhances topological stability.
• * Accounting for site-specific sequence heterogeneity improves the resolution of previously intractable phylogenetic relationships.
• * The refined phylogenomic framework provides a more stable and reliable evolutionary history for the Aphidinae.

Conclusions:

• * This research offers a refined evolutionary framework for the Aphidinae subfamily.
• * The study highlights the crucial role of rigorous data curation and filtering in resolving complex evolutionary radiations.
• * Findings contribute to a better understanding of aphid diversification and pest management strategies.