Phylogeography of Popillia japonica

This repository contains Variant Call Format (VCF) files generated from whole-genome sequencing of 83 individuals of Popillia japonica (Japanese beetle). These VCF files represent high-resolution genomic variation data, capturing single nucleotide polymorphisms (SNPs) across the sampled individuals. The dataset is intended to support studies on population genomics, genetic diversity, and the evolutionary history of P. japonica, facilitating analyses of invasion pathways, demographic events, and adaptation processes in this invasive species. Additionally, .txt files of a sample name list (names_list_pj), and a file containing NCBI sample names, VCF sample names, area and locality (names_and_population), are also provided as metadata of the VCF files. The folder 'genome' contains the genome file with associated metadata (masking of repeat elements, list of contigs used for variant calling) as used in the analysis. The folder 'Fastsimcoal2_tpl_est_files' provides .tpl and .est files for all models (subset 1 only, additional subsets may eventually differ for the number of selected segregating sites during mSFS production) and those for parameter estimation (from best model).In supplement to: Funari, R., Parvizi, E., Cucini, C., et al. (2025). Whole genome resequencing reveals origins and global invasion pathways of the Japanese beetle Popillia japonica. Molecular Ecology