(A) Categories of regulatory divergence between M. m. musculus and M. m. domesticus inferred from gene expression levels in pure subspecies and hybrids, where P and H are the ratio of reads mapping to M. m. domesticus versus M. m. musculus in the pure species and hybrids, respectively. (B) The relative distribution of regulatory categories in this data set. Each point represents one gene. Points represent log₂ fold changes between reads mapping to each allele in the hybrid (M. m. domesticus/M. m. musculus) and the reads mapping to each subspecies (M. m. domesticus/M. m. musculus). Genes are color-coded based on their inferred regulatory category.