Large-scale genomic variation analysis reveals evolutionary patterns and adaptive mechanisms across 98 insects

Background: Insects represent the most diverse group of animals and have achieved remarkable evolutionary success across a wide array of ecological niches. Their adaptability is largely attributed to extensive genomic variation. However, the evolutionary forces shaping this variation remain inadequately understood.
Results: Here, we perform a large-scale comparative analysis of genomic variation across six orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera, Hemiptera, and Phasmatodea) using 3,187 high-quality resequencing datasets from 98 insects. To uncover the lineage-specific mutation rates and evolutionary constraints, we characterize genome-wide single nucleotide polymorphisms (SNPs) and insertion-deletion variants (InDels). The results showed that Coleoptera exhibits the highest SNP and InDel rates, ranging from 10⁻³ to 10⁻⁷ and 10⁻⁴ to 10⁻⁷, respectively. This partially explains the species richness of this order, whereas domesticated Diptera and Hymenoptera show reduced variation. In addition, transition-transversion ratios vary markedly among insects. Functional analyses of high-diversity genes highlight key orthogroups related to transposon, odorant receptors , and cytochrome P450.
Conclusions: These findings suggest that transposon dynamics, selective pressures on genomic regions associated with chemoreception and detoxification, and lineage-specific variation collectively drive insect adaptation. Our study offers new insights into the genomic basis of insect diversification and has important implications for predicting adaptive responses to environmental change as well as for developing targeted pest management strategies.