Phylogeography of <i>Popillia japonica</i>

This repository contains Variant Call Format (VCF) files generated from whole-genome sequencing of 83 individuals of <i>Popillia japonica</i> (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 <i>P. japonica</i>, 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 <i>Popillia japonica</i>. Molecular Ecology<br>

本仓库包含从83头日本弧丽金龟（*Popillia japonica*，日本甲虫）个体的全基因组测序数据中生成的变异检测格式（Variant Call Format, VCF）文件。这些VCF文件呈现高分辨率基因组变异数据，涵盖所有采样个体的单核苷酸多态性（single nucleotide polymorphisms, SNPs）。
本数据集旨在支撑日本弧丽金龟的种群基因组学、遗传多样性及演化历史相关研究，助力该入侵物种的入侵路径、种群动态事件与适应性过程等分析。
此外，本仓库还提供了作为VCF文件元数据的两类文本文件：其一为样本名称列表文件（names_list_pj），其二为包含NCBI样本名称、VCF样本名称、采样区域与地点的元数据文件（names_and_population）。
“genome”文件夹内含本次分析所用的基因组文件及相关元数据，包括重复序列屏蔽信息、变异检测所用的重叠群（contig）列表。
“Fastsimcoal2_tpl_est_files”文件夹提供两类文件：一是仅包含子集1的所有模型的.tpl和.est文件（其余子集在制作mSFS时所选的分离位点数量可能存在差异），二是基于最优模型的参数估计所需文件。
本数据集为下述论文的补充数据：Funari, R.、Parvizi, E.、Cucini, C. 等（2025）. 全基因组重测序揭示日本弧丽金龟（*Popillia japonica*）的起源与全球入侵路径. 《分子生态学（Molecular Ecology）》

搜集汇总

背景与挑战

背景概述

该数据集包含83只日本甲虫（Popillia japonica）个体的全基因组测序生成的VCF文件，捕获了高分辨率基因组变异数据（SNPs），旨在支持种群基因组学、遗传多样性和进化历史研究，特别是分析这种入侵物种的入侵途径、人口统计事件和适应过程。数据集还包括元数据、基因组文件和模型文件，与一篇关于日本甲虫起源和全球入侵途径的分子生态学论文相关，适用于生物地理学和基因组学领域的研究。