An updated phylogenomic tree of Coleoptera (beetles)

Resolving deep phylogenetic relationships within Coleoptera remains challenging despite recent advances in phylogenomics. Here, we reconstruct relationships among beetle lineages to the subfamily level and evaluate how locus filtering, substitution models, and matrix completeness affect the recovered topology. We assembled an updated phylogenomic dataset integrating available genome assemblies, reprocessed short-read data, and newly generated genomes. The dataset comprises 263 beetle species representing 104 families and 210 subfamilies, together with 13 outgroups, based on 2,280 orthologous loci selected from a Coleoptera-specific BUSCO dataset. A multi-step pipeline optimised orthology assignment, alignment quality, and locus selection, incorporating sequence- and tree-based filtering criteria to minimise the effects of compositional heterogeneity, rate variation, and model misspecification. Phylogenetic analyses of concatenated datasets recovered highly congruent topologies across substitution models and recoding schemes for matrices with 50-70% taxon occupancy, whereas more stringent occupancy thresholds (≥90%) reduced phylogenetic accuracy due to substantial data loss. The preferred topology obtained under the PMSF model supports the basal split between Polyphaga and the remaining suborders and recovers the principal early-diverging lineages of Polyphaga. Relationships among polyphagan infraorders are largely consistent with previous phylogenomic studies, while substantially extending taxonomic resolution to the subfamily level. Uncertainty remains regarding basal relationships within Elateroidea, Staphylinidae, Curculionidae, and the superfamily-level relationships within Cucujiformia. Stringent locus filtering increased gene concordance despite broadly consistent topologies recovered from the excluded loci. The GHOST mixture model yielded several plausible alternative relationships, whereas coalescent approaches using ASTRAL produced less consistent deep-level topologies. Low gene concordance factors highlighted the remaining weakly supported nodes across the tree. These results provide an expanded phylogenomic framework for Coleoptera and underscore the importance of balanced taxon sampling, rigorous data curation, and appropriate evolutionary model selection for resolving ancient insect radiations.