Sequential accumulation of adaptive alleles forms an inversion supergene in deer mice

Supergenes are clusters of co-inherited loci that affect multiple or complex phenotypes. Despite the growing number of chromosomal inversions identified as supergenes in natural populations, their molecular basis and evolutionary history often remain obscure. Here, we identified two candidate genes, Slc45a2 and Npr3 , within a 41-Mb inversion supergene in the deer mouse ( Peromyscus maniculatus ) that respectively drive darker coats and longer tails—two traits associated with forest adaptation. Mice homozygous for the inversion ( inv/inv ) exhibit elevated Slc45a2 expression in melanocytes relative to the congenic standard genotype ( std/std ), disrupting pheomelanin production. In parallel, downregulation of Npr3 in inv/inv mouse growth plates prolongs postnatal growth of caudal vertebrae, resulting in tail elongation. Population-level analyses further implicate that this supergene arose through the subsequent accumulation of the Npr3 allele within the inversion, rather than by capturing all beneficial mutations at its origin.