Development translates genetic variation into a multivariate pattern of phenotypic variation, distributing it among traits in a nonuniform manner. As developmental processes are largely shared within species, this suggests that heritable phenotypic variation will be patterned similarly, in spite of the different segregating alleles. To investigate developmental effect on the variational pattern in the shape of the mouse skull across genetically differentiated lines, we employed the full set of reciprocal crosses (a.k.a. diallel) between eight inbred mouse strains of the Collaborative Cross Project. We used geometric morphometrics and multivariate analysis to capture cranial size and shape changes in 8 parentals and their 54 F1 crosses. The high heterozygosity generated in the F1 crosses allowed us to compare the multivariate deviations of the F1 phenotypes from the expected midparental phenotypes in different haplotype combinations. In contrast to body weight, we found a high degree of nonadditive deviation in craniofacial shape. Whereas the phenotypic and genetic divergence of parental strains manifested in high dimensionality of additive effects, the nonadditive deviations exhibited lesser dimensionality and in particular a strikingly coherent direction in shape space. We interpret this finding as evidence for a strong structuring effect of a relatively small set of developmental processes on the mapping of genetic to phenotypic variation.
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