Data from: Using the Mus musculus hybrid zone to assess covariation and genetic architecture of limb bone lengths

Two subspecies of the house mouse, Mus musculus domesticus and Mus
musculus musculus, meet in a narrow contact zone across Europe. Mice in
the hybrid zone are highly admixed, representing the full range of mixed
ancestry from the two subspecies. Given the distinct morphologies of these
subspecies, these natural hybrids can be used for genome-wide association
mapping at sufficiently high resolution to directly infer candidate genes.
We focus here on limb bone length differences, which is of special
interest for understanding the evolution of developmentally correlated
traits. We used 172 first-generation descendants of wild-caught mice from
the hybrid zone to measure the length of stylopod (humerus / femur),
zeugopod (ulna / tibia) and autopod (metacarpal / metatarsal) elements in
skeletal CT scans. We find phenotypic covariation between limb elements in
the hybrids similar to patterns previously described in M. m. domesticus
inbred strains, suggesting that the hybrid genotypes do not influence the
covariation pattern in a major way. Mapping was performed using 143,592
SNPs and identified several genomic regions associated with length
differences in each bone. Each candidate region explains only a small
proportion of phenotypic variance, suggesting that bone length is highly
polygenic. None of the candidate regions includes the canonical genes
known to control embryonic limb development. Instead, we are able to
identify candidate genes with known roles in osteoblast differentiation
and bone structure determination, as well as recently evolved genes of, as
yet, unknown function.