Demographic history inferred from an inversion-rich spruce bark beetle genome

The demographic history of species inferred from whole-genome data provides quantitative insights into key biological parameters such as population size changes and divergence times. Reliable estimates often require data that have not been affected by selection. Extensive research, however, indicates that many species harbour multiple polymorphic chromosomal inversions, which often evolve under different selective pressures. Consequently, inversions can influence genome-wide patterns of variation and subsequent evolutionary inferences. In this study, we used genome-wide data from over 300 spruce bark beetle (Ips typographus) individuals from 23 populations across Europe to reconstruct their demographic history and to investigate the impact of a complex polymorphic inversion landscape (covering approximately 28% of the beetle genome) on demographic inference. We used two complementary methods, Pairwise Sequential Markovian Coalescent (PSMC) and Site Frequency Spectrum (SFS)-based modelli..., , # Data from: Demographic history inferred from an inversion-rich spruce bark beetle genome Dataset DOI: [10.5061/dryad.3ffbg7b01](https://doi.org/10.5061/dryad.3ffbg7b01) ## Description of the data and file structure **Associated publication:** *Demographic history inferred from an inversion-rich spruce bark beetle genome* **Raw sequencing data availability:** Raw FASTQ files are deposited in the NCBI Sequence Read Archive (SRA) and are available under BioProject ID PRJNA1013983. ### **General information** This repository contains data files and analysis pipelines used for population genomic and demographic analyses of *Ips typographus*. The materials include workflows for raw sequencing data processing, variant calling, site frequency spectrum (SFS) construction, and demographic inference using both SFS-based (fastsimcoal2) and Pairwise Sequentially Markovian Coalescent (PSMC) based approaches. Processed variant call data (VCF format) and scripts are provided to facilitate tran...,