A chromosomal inversion accumulates adaptive and barrier loci in a cold-adapted insect species

Chromosomal inversions can play a crucial role in population adaptation and divergence by reducing gene flow and preserving adaptive allelic combinations between populations or ecotypes that carry alternative arrangements. However, demonstrating this empirically remains challenging because of the numerous interacting processes with similar genomic signatures that can influence inversion evolution. In this study, we characterize a large (9.5Mb) polymorphic inversion in the cold-adapted and widely distributed insect species, Drosophila montana , using a combination of long- and short-read sequencing across several populations. The origin of this inversion predates the divergence of North American (NA) and Fennoscandian (North European) populations, indicating that it emerged in the ancestral D. montana population in the Rocky Mountains of North America. Despite the species’ expansion across the northern hemisphere, this inversion has remained exclusive to the Rocky Mountain populations, where it is fixed in the southernmost high-elevation population and appears at lower frequencies in the more northern and lower-elevation populations. By independently mapping SNPs associated with climate and cold adaptation and barrier regions that restrict gene flow, we found that the inversion acts as a hotspot for both, with the barrier and adaptive regions partially overlapping. Overall, the enrichment of adaptive and barrier loci, along with its exclusive presence in Rocky Mountain populations, strongly suggests that chromosomal inversions play a key role in environmental adaptation by restricting gene flow and facilitating adaptive divergence between populations.