Population genomic signatures of the oriental fruit moth related to the Pleistocene climates

The oriental fruit moth is a pest species native to East Asia with refugial and colonized populations throughout the region. Here, a chromosome-level assembly for the species is reported and used to identify genomic signatures related to Quaternary climate change. The Quaternary climatic oscillations are expected to have had strong impacts on the evolution of species. Although legacies of the Quaternary climates on population processes have been widely identified in diverse groups of species, adaptive genetic changes shaped during the Quaternary have been harder to decipher. Here, we assembled a chromosome-level genome of the oriental fruit moth and compared genomic variation among refugial and colonized populations of this species that diverged in the Pleistocene. High genomic diversity was maintained in refugial populations. Demographic analysis showed that the effective population size of refugial populations declined during the penultimate glacial maximum (PGM) but remained stable during the last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified one chromosomal inversion and a mutation of the circadian gene Clk on the neo-Z chromosome potentially related to the endemicity of a refugial population. In the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection. These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species.

Automated summary

This study reports the chromosome-level assembly of the oriental fruit moth genome and investigates genomic variation between refugial and colonized populations. The results reveal strong impacts of Quaternary climates on the evolution of this species, with high genomic diversity in refugial populations and distinct gene variations associated with specific refugial populations. In the colonized populations, genes related to energy metabolism and wing development show selection signatures.