Refined Phylogenomics Resolves Discordance in the Aphidinae Phylogeny

Area of Science:

• * Entomology
• * Evolutionary Biology
• * Genomics

Background:

• * Aphids are significant agricultural pests, causing substantial economic damage worldwide.
• * The internal phylogeny of the Aphidinae subfamily, particularly intergeneric relationships and tribal boundaries, remains poorly understood.
• * Previous phylogenetic studies have faced challenges due to conflicting data and complex evolutionary patterns.

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.
• * Comparative phylogenomic analyses using datasets of varying sizes (157 taxa vs. 47 taxa) and evaluation of sequence properties influencing phylogenetic conflict.

Main Results:

• * Filtering phylogenetically inconsistent genomic loci significantly enhances topological stability.
• * Accounting for site-specific sequence heterogeneity improves the resolution of recalcitrant taxa.
• * The refined phylogenomic framework clarifies intergeneric relationships and tribal boundaries within Aphidinae.

Conclusions:

• * This study provides a more accurate evolutionary framework for the Aphidinae subfamily.
• * Highlights the essential role of rigorous data curation and filtering in resolving complex phylogenies.
• * Offers insights into the evolutionary dynamics of rapid radiations in agriculturally important pests.