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In fossil hominins, phyletic diversification – the process by which ancestral species give rise to descendant ones – can only be inferred through analysis of patterns of morphological diversity displayed in the fossil record. These patterns are interpreted typically in terms of selection/adaptation and related to environmental change. From an organism-centered perspective, evolutionary modification of developmental processes is an equally important source of phyletic diversity. Here, we use model systems to simulate cranial growth and to explore how mutations in the “genes” of an “ancestral” morphogenetic system may affect “descendant” ontogenies and “adult” morphologies. Intriguingly, a model that assumes basic epigenetic interactions between developmental processes is capable of producing a wide variety of patterns of developmental modification, many of which are not foreseen in classic heterochronic theory. Also, small changes in developmental “genes” often have complex effects on patterns of ontogeny. With regard to the evolutionary split between Neanderthals and modern humans, these model considerations shall be an incentive to look at taxon-specific character complexes from the perspective of developmental as opposed to functional constraints.