Natural and artificial selection generate distinct cranial diversification pathways in bats and domestic dogs

How far can evolution push a complex structure before hitting developmental limits, and when can it break free to explore new forms? Domestic dogs (Canis familiaris) represent the most extreme skull shape diversity generated within a single species through recent artificial selection, while neotropical leaf-nosed bats (Phyllostomidae) showcase the broadest craniofacial radiation in mammals, shaped over millions of years of natural selection. Because these contrasting systems belong to the same mammalian superorder, they provide an opportunity to test whether skull evolution is constrained by the same limits operating at short timescales, or whether adaptive radiations enable access to novel morphologies at macroevolutionary scales. Using three-dimensional geometric morphometrics of 33 canids (dog breeds and wild species) and 62 phyllostomid species, we mapped cranial variation across morphospace to assess disparity and modularity, and then compared the dominant directions of cranial shape variation between clades. Despite the overlap in morphospace for some bats and dogs, we found numerous examples of evolutionary novelty in bats, supporting the emergence of macroevolutionary innovation. Both clades varied along a primary axis of snout elongation and shortening, but with distinct outcomes: the slightly more modular canine skull was largely confined to a single dominant direction of variation, whereas phyllostomids dispersed along multiple axes while occupying regions inaccessible to dogs despite exhibiting stronger cranial integration. While artificial selection in dogs has produced much more disparity per unit of evolutionary time, natural selection in bats reveals repeated evolutionary innovations rather than constrained scaling. These results demonstrate that artificial selection may inflate variation along a constrained axis, while natural selection may allow structural innovation beyond the limits of microevolutionary change.