Large Scale Insect Phylogenomics Analyses reveal new insights into insect Evolution

Understanding insect evolution requires resolving deep phylogenetic relationships and divergence times, yet conflicting hypotheses persist due to biological and methodological complexities. Here, we address this challenge by reconstructing a robust, time-calibrated phylogeny of Insecta using 481 single-copy orthologous genes from 794 high-quality genomes. Our analyses resolve most inter-ordinal relationships with high confidence and employ a multi-faceted approach to diagnose the nature of two contentious nodes. We show that the conflict surrounding the relationships among Paraneoptera is the result of a hard polytomy, consistent with an ancient radiation event where phylogenetic signal is genuinely absent. In contrast, the conflict at the base of Holometabola is characterized by a dominant signal competing with a significant secondary one, a pattern consistent with deep coalescence that allows for a statistically confident resolution. Our divergence time estimates place the origin of insects in the Early Ordovician (~469 Ma) and the evolution of flight in the Silurian, coinciding with the rise of terrestrial vascular plants. Ultimately, our study provides a comprehensive framework for the insect tree of life and demonstrates how moving beyond a single topological estimate to diagnose the distinct evolutionary processes underlying phylogenomic conflict can resolve key relationships and explain the sources of persistent incongruence.