A genome-based framework for the insect tree of life reveals the distinct biological drivers of phylogenomic conflict

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 leveraging 794 high-quality genomes to reconstruct a robust, time-calibrated phylogeny of Insecta using 481 strictly defined single-copy orthologous genes, effectively minimizing the missing-data artifacts often prevalent in broad transcriptomic studies. Our analyses resolve most inter-ordinal relationships with high confidence and employ a multi-faceted framework to diagnose the nature of phylogenomic conflict at two historically contentious nodes. We provide evidence that the instability surrounding the relationships among Paraneoptera stems from a hard polytomy, consistent with an ancient rapid radiation event where dichotomous phylogenetic signal is largely absent. In contrast, the conflict regarding the placement of Strepsiptera (sister to Coleoptera) is characterized by a dominant signal competing with a significant secondary one, a pattern consistent with incomplete lineage sorting (ILS) that allows for a statistically confident resolution. Importantly, by incorporating recent critical fossil discoveries and implementing permissive minimum-age constraints, our updated divergence time estimates place the origin of winged insects in the Early Ordovician (~477 Ma), a timeline synchronous with the initial terrestrialization of early land plants. Ultimately, our study provides a rigorously updated genome-based framework for the insect tree of life and demonstrates how distinguishing between different evolutionary processes can resolve key relationships and explain sources of persistent incongruence.