Phylogenomic datasets can produce apparently decisive insect phylogenies while retaining substantial uncertainty about the histories represented by individual loci, the adequacy of sampled data, and the assumptions linking gene trees to species trees. This article develops a framework for distinguishing uncertainty generated by biological gene-tree heterogeneity, missing taxa or loci, orthology error, model misspecification, and downstream species-tree inference. The central argument is that conventional branch support cannot function as a universal summary of these distinct uncertainties. Gene-tree discordance may represent incomplete lineage sorting, introgression, duplication and loss, or analytical error; missingness may interact with taxon representation and phylogenetic information rather than operate as a simple percentage threshold; and apparent orthology can be disrupted by differential gene loss without making all multicopy data unusable. Model adequacy introduces a further boundary between strongly supported inference and adequately represented evolutionary processes. The proposed uncertainty-source architecture therefore separates the origin of uncertainty, its observable manifestation, the inference stage it can affect, and the degree to which it remains unresolved after species-tree estimation. The framework does not assign numerical certainty grades or identify a single correct topology. Instead, it establishes a basis for reporting when confidence is localized to a statistical procedure while biological or analytical alternatives remain unresolved. Explicitly preserving those alternatives should make insect phylogenomic conclusions more interpretable, reproducible, and appropriately conditional.
