Data from: Use of a natural hybrid zone for genome-wide association mapping of craniofacial traits in the house mouse

The genetic pathways underlying natural variation in morphology are still poorly known, hampering our understanding of the evolution of shape. Here we explore a new approach using samples from a natural hybrid zone between two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus) for the mapping of an ecologically relevant trait. Due to the long history of recombination of genotypes in the hybrid zone, a high mapping resolution can be anticipated. Furthermore, the combination of genomes from subspecies allows the mapping of not only intra-specifically segregating, but also inter-specific fixed variants. To map the craniofacial traits, skull and mandible shape were phenotyped using 3D landmarks and geometric morphometrics. Genotyping was achieved with a high density SNP chip. Using PC-axes as phenotypes and a linear mixed model to account for genetic relatedness in the mapping populations, we identified 9 genomic regions associated with skull and 10 with mandible shape. Mapping resolution (median size of significant regions = 148 kb) enabled identification of single or few candidate genes in most cases. One extended region on chromosome 8 includes multiple genes acting as regulators or modifiers of signaling pathways relevant for morphological development and bone formation, including several with known craniofacial phenotypes in mice and humans. Our results are consistent with a polygenic basis for craniofacial shape variation, and confirm that mapping in hybrid zones can be a powerful tool to explore the genetics of complex traits in natural populations.