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Abstract The potential of artificial selection to dramatically impact phenotypic diversity is well known. Large-scale morphological changes in domestic species, emerging over short timescales, offer an accelerated perspective on evolutionary processes. The domestic horse (Equus caballus) provides a striking example of rapid evolution, with major changes in morphology and size likely stemming from artificial selection. However, the microevolutionary mechanisms allowing to generate this variation in a short time interval remain little known. Here, we use 3D geometric morphometrics to quantify skull morphological diversity in the horse, and investigate modularity and integration patterns to understand how morphological associations contribute to cranial evolvability in this taxon. We find that changes in the magnitude of cranial integration contribute to the diversification of the skull morphology in horse breeds. Our results demonstrate that a conserved pattern of modularity does not constrain large-scale morphological variations in horses and that artificial selection has impacted mechanisms underlying phenotypic diversity to facilitate rapid shape changes. More broadly, this study demonstrates that studying microevolutionary processes in domestic species produces important insights into extant phenotypic diversity.

Abstract Background Hybridization has been widely practiced in plant and animal breeding as a means to enhance the quality and fitness of the organisms. In domestic equids, this hybrid vigor takes the form of improved physical and physiological characteristics, notably for strength or endurance. Because the offspring of horse and donkey is generally sterile, this widely recognized vigor is expressed in the first generation (F1). However, in the absence of recombination between the two parental genomes, F1 hybrids can be expected to be phenotypically intermediate between their parents which could potentially restrict the possibilities of an increase in overall fitness. In this study, we examine the morphology of the main limb bones of domestic horses, donkeys and their hybrids to investigate the phenotypic impact of hybridization on the locomotor system. We explore bone shape variation and covariation to gain insights into the morphological and functional expressions of the hybrid vigor commonly described in domestic equids. Results Our data reveal the occurrence of transgressive effects on several bones in the F1 generation. The patterns of morphological integration further demonstrate that the developmental processes producing covariation are not disrupted by hybridization, contrary to functional ones. Conclusions These results suggest that an increase in overall fitness could be related to more flexibility in shape change in hybrids, except for the main forelimb long bones of which the morphology is strongly driven by muscle interactions. More broadly, this study illustrates the interest of investigating not only bone shape variation but also underlying processes, in order to contribute to better understanding how developmental and functional mechanisms are affected by hybridization.