Phylostratigraphic Analysis Reveals the Evolutionary Origins and Potential Role of New Genes in the Adaptive Evolution of Spodoptera frugiperda

The fall armyworm, <i>Spodoptera frugiperda</i>, has become one of the most damaging agricultural pests worldwide, yet the genetic basis of its extraordinary adaptability remains elusive. Recent studies have highlighted the pivotal role of newly evolved genes in adaptive evolution, and phylostratigraphy has emerged as a powerful conceptual framework to trace their origins. Here, we adopt this framework to investigate how new genes have contributed to the rapid adaptive evolution of <i>S. frugiperda</i>. Using high-quality genomic data, we inferred gene ages across evolutionary phylostrata and identified 277 newly evolved genes that originated after the divergence of <i>Spodoptera</i>. These new genes exhibit hallmark genomic signatures of recent origin, including shorter coding regions, simplified structures, and relaxed evolutionary constraints. Interestingly, transcriptomic analyses revealed strong tissue specificity, with pronounced enrichment in the antenna and brain, indicating possible involvement in chemosensory and neural functions essential for environmental and behavioral adaptation. Under diverse environmental challenges such as pesticide and parasitoid wasp exposure, and virus infection, we found many of the new genes acted as hubs in the regulatory networks associated with pesticide response. Together, our findings suggest that the emergence of new genes has played a critical role in shaping the rapid adaptive evolution of <i>S. frugiperda</i> and provide broader insights into how newly evolved genes contribute to species adaptation.