Massive inversion polymorphisms shape the genomic landscape of deer mice

Chromosomal inversions are an important form of structural variation that can affect recombination, chromosome structure and fitness. However, because inversions can be challenging to detect, the prevalence and hence significance of inversions segregating within species remains largely unknown, especially in natural populations of mammals. Here, by combining population-genomic and long-read sequencing analyses in a single, widespread species of deer mouse (Peromyscus maniculatus), we identified 21 polymorphic inversions, which are large (1.5-43.8 Mb) and cause near complete suppression of recombination when heterozygous (0-0.03 cM/Mb). We found that inversion breakpoints frequently occur in centromeric and telomeric regions and are often flanked by long inverted repeats (0.5-50 kb), suggesting that they likely arose via ectopic recombination. By genotyping the inversions in populations across the species range, we found that the inversions are often widespread, do not harbor deleterious mutational loads, and many are likely maintained as polymorphisms by divergent selection. Comparisons of forest and prairie ecotypes of deer mice revealed 13 inversions that contribute to differentiation between populations, of which five exhibit significant associations with traits implicated in local adaptation. Together, we found that inversion polymorphisms have a significant impact on recombination, genome structure and genetic diversity in deer mice, and likely facilitate local adaptation across this species widespread range.