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

<p><span class="fontstyle01"><span>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 </span></span>assembled a chromosome-level genome<span class="fontstyle01"><span> 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.</span></span> <span class="fontstyle01"><span>Demographic analysis showed that the effective population size of refugial populations declined during the </span></span><span class="fontstyle01"><span>penultimate glacial </span></span><span class="fontstyle01"><span>maximum (PGM) </span></span><span class="fontstyle01"><span>but remained stable during the </span></span><span class="fontstyle01"><span>last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified </span></span>one chromosomal inversion<span class="fontstyle01"><span> and a mutation of the </span></span><span class="fontstyle01"><span>circadian gene </span></span><span class="fontstyle01"><span><i>Clk</i></span></span><span class="fontstyle01"><span> on the neo-Z chromosome</span></span> potentially related to the <span class="fontstyle01"><span>endemicity of </span></span>a refugial population.<span class="fontstyle01"><span> I</span></span><span class="fontstyle01"><span>n the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection</span></span><span class="fontstyle01"><span>.</span></span><span class="fontstyle01"><span> These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species.</span></span></p>