Rapid insect radiations are a severe test of phylogenomic inference because large genomic matrices can yield strongly supported species-tree hypotheses while retaining extensive conflict among genes, sites, marker classes, or analytical models. This methodological review evaluates how taxon sampling, locus selection, missing data, orthology assessment, paralogy, gene-tree estimation, model choice, and introgression-aware analyses jointly condition interpretation of discordance. Evidence from aphids, alpine butterflies, cicadas, leafhoppers, sawflies, tephritid flies, hymenopterans, and broader methodological studies indicates that no single diagnostic resolves all short-internode radiations. The central synthesis proposed here is a design-conditional interpretation of discordance: biological explanations should be considered only after plausible pipeline-generated contributions have been stress-tested. In this view, support values summarize confidence under a specified analysis but do not by themselves distinguish incomplete lineage sorting, gene flow, hidden paralogy, missingness, model misspecification, or gene-tree error. Robust phylogenomic inference therefore depends on the stability of conclusions across defensible sampling and model perturbations and on concordance among evidence classes that make different assumptions. This approach preserves uncertainty where historical processes remain statistically non-identifiable and avoids treating a single preferred topology as complete resolution of a rapid radiation.
