Data from: 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.