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

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 endem..., Samples

A laboratory-reared strain of the OFM was used for de novo genome sequencing. This strain derived from three male and female pairs and had been maintained for ten generations on apples in laboratory conditions. We collected 263 individuals from 15 geographical populations across the native range of the OFM in China, of which three populations were collected from Sichuan basin, three populations were from the Yunnan region, and six populations were from regions where OFM subsequently dispersed (Table S1, Fig. 2). We chose three representative populations (31 individuals in total) for whole-genome resequencing; one population (YNHH) was collected from the original and refugial area in Yunnan, one (SCCD) was from another refugial area in Sichuan, while the last population (BJPG) was from colonized areas of northern China (Table S1 and Fig. 2). The other 12 populations (232 individuals) were genotyped by the Kompetitive Allele-Specific PCR (KASP) method for 22 representative SNP ...,