Data from: Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest

Background: Refugial populations in Quaternary glaciations are critical to understanding the evolutionary history and climatic interactions of many extant species. Compared with the well-studied areas of Europe and Northern America, refugia of species in eastern Asia remain largely unknown. Here, we investigated the phylogeographic history of a globally important insect pest, the oriental fruit moth Grapholita molesta, in its native range of China. Results: Genetic structure analyses unveiled three distinct groups and a set of populations with admixture. Approximate Bayesian Computation (ABC) analyses support range expansion of this moth from southwest groups of Yunnan and Sichuan to northern and eastern China. A set of admixed populations was found around these two ancestral groups. This pattern of genetic structure points to two refugia located in the Yunnan region and Sichuan Basin. The split of the two refugia was dated to 329.2 thousand years ago in the penultimate glacial period. One of the lineages was exclusively found around the Sichuan Basin, indicating the formation of endemic populations in this refugium. Ecological niche model analysis suggested a shrinking distribution from the past to the present in the Sichuan lineage but a wide and stable distribution in the other lineage. Conclusions: Our results for the first time suggest that Yunnan and Sichuan jointly served as two large-scale refugia in eastern Asia in Quaternary glaciations, helping to maintain genetic diversity overall.Microsatellite loci genotyped from each individual01_microsatellite_loci_genotyped_from_each_individual.genepopAligned mitochondrial genes from all individuals02_aligned_mitochondrial_genes_from_all_individuals.fasMitochondrial haplotypes used for SplitsTree analysis03_mitochondrial_haplotypes_used_for_SplitsTree_analysis.nexMitochondrial haplotypes used for molecular dating using BEAST04_mitochondrial_haplotypes_used_for_molecular_dating_using_BEAST.fasInputfile for BAPS and STRUCTURE analysesinput_files_of_BAPS_STRUCTURE.rarR script for DAPC analysis09_R_script_for_DAPC_analysis.RFiles for DIYABC analysesfiles for DIYABC analyses.rarCommands used in IMa2 analysis12_commands_used_in_IMa2_analysis.txtScripts and input files used in IBD analysisscripts and input files used in IBD analysis.ra