Population genetics of saproxylic beetle assemblages in protected and managed forests

This dataset contains filtered single nucleotide polymorphism (SNP) datasets derived from raw data generated using double-digest RAD sequencing (ddRAD-seq) for multiple saproxylic beetle species sampled across Central European forests. Data are provided as species-specific Variant Call Format (VCF) files, which can be opened and inspected using standard genomic software such as VCFtools, bcftools, and PLINK, and visualised using tools such as IGV.The SNP datasets were generated through the Stacks pipeline and subsequently filtered for downstream population genetic analyses. The VCF files were used for analyses including population structure, genetic diversity, and differentiation, using commonly applied software such as PLINK, vcftools, and R packages (e.g. adegenet, vcfR).Associated metadata include species identity, forest, sampling sites, geographic coordinates of sites, and information on forest management type for each site. The dataset is made publicly available to ensure transparency, reproducibility, and long-term accessibility of the analyses, and to allow reuse of the SNP data in future population genomic and conservation studies.