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 modelling, and revealed a Late Pleistocene divergence (∼79 kya) between populations from the southern and northern parts of the species’ European range, and a long-term effective population size of ∼250,000. The southern group underwent significant population expansion after this divergence event, whereas the northern group expanded during the Holocene (∼7 kya). Recent population size estimates suggest that the southern group is twice as large as the northern group. Neglecting the presence of chromosomal inversions did not significantly affect the model selection procedure and resulted in relatively small biases in the estimated demographic parameters. This study provides information on the historical population dynamics of the spruce bark beetle and improves our understanding of the influence of a complex genomic architecture on the inference of evolutionary history.