Field evolved resistance to insecticides is one of the main challenges in pest control. The fall armyworm (FAW) is a lepidopteran pest species causing severe crop losses, especially corn. While native to the Americas, the presence of FAW was confirmed in West Africa in 2016. Since then, the FAW has been detected in over 70 countries covering sub-Saharan Africa, the Middle East, North Africa, South Asia, Southeast Asia, and Oceania. In this study, we tested whether this invasion was accompanied by the spread of resistance mutations from native to invasive areas. We observed that mutations causing Bt resistance at ABCC2 genes were observed only in native populations where the mutations were initially reported. Invasive populations were found to have higher gene numbers of cytochrome P450 genes than native populations and a higher proportion of multiple resistance mutations at acetylcholinesterase genes, supporting strong selective pressure for resistance against synthetic insecticides. This result explains the susceptibility to Bt insecticides and resistance to various synthetic insecticides in Chinese populations. These results highlight the necessity of regular and standardized monitoring of insecticide resistance in invasive populations using both genomic approaches and bioassay experiments.

Copy number variations (CNVs) are major sources of genetic variation, affecting large portions of genomes. Typical CNVs are known to have short evolutionary half-lives due to deleterious effects, with documented events of adaptive evolution. However, it is not known whether the same trends apply to CNVs preserving intact Open Reading Frames (iORF-CNVs), which can encode functional proteins. Here, we investigate the mechanistic origins and evolutionary dynamics of iORF-CNVs in Spodoptera frugiperda, a globally distributed pest species where CNV-mediated adaptive evolution has been reported. Using PacBio HiFi reads, we generated high-quality, individually assembled genomes for 36 field-collected individuals and identified 349 genes with polymorphic iORF-CNVs. These elements are short, intronless, and display molecular signatures of LINE-mediated retrotransposition, including cis- and trans-acting effects. A majority of iORF-CNVs (68.0% to 77.28%) exhibited at least one molecular signature of retrotransposition. iORF-CNVs showed lower divergence at the first and second codon positions than at the third codon positions, but they had higher nonsynonymous-to-synonymous polymorphism ratios than non-iORF-CNV genes, implying purifying selection with relaxed constraint. Orthology analyses indicated that these CNVs originate from genes under weak evolutionary constraint, while transcriptomic and promoter motif analyses revealed that many are transcribed and retain regulatory features. We conclude that observed iORF-CNVs are generated through retrotransposition from weakly constrained genes and that the duplicates are selectively maintained for coding potential, albeit under reduced purifying selection compared with non-iORF-CNV genes. These results imply that pseudogenization is not an inevitable evolutionary fate of retrotransposed gene copies when the open reading frame is preserved.