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standing the old. This is a reflection of the way evolution works, with some novelties being traceable as modifications of primitive conditions and others having origins that are much less obvious. As a result, the problems of novelty and homology have been deeply intertwined for the past century and a half. It is here, at the interface between these two great concepts of evolutionary biology, where fresh data from developmental biology have had an extraordinary impact. One of the most important, and entirely unanticipated, insights of the past 15 years was the recognition of an ancient similarity of patterning mechanisms in diverse organisms, often among structures not thought to be homologous on morphological or phylogenetic grounds. In 1997, prompted by the remarkable extent of similarities in genetic regulation between organs as different as fly wings and tetrapod limbs, we suggested the term ‘deep homology’ to describe the sharing of the genetic regulatory apparatus that is used to build morphologically and phylogenetically disparate animal features. Homology, as classically defined, refers to a historical continuity in which morphological features in related species are similar in pattern or form because they evolved from a corresponding structure in a common ancestor. Deep homology also implies a historical continuity, but in this case the continuity may not be so evident in particular morphologies; it lies in the complex regulatory circuitry inherited from a common ancestor. In some instances, recognition of deep homologies can help in the identification of cryptic classical homologies, when morphological data alone are inadequate to make the case for homology. For example, the photoreceptors present in various extant clades would not be recognized as homologous without the observation of common underlying genetic cassettes (discussed in the next section). Deep homology, however, can also be found in contexts in which structures are not homologous in the classical sense. As we explored in 1997, appendages in vertebrates, arthropods and other bilaterians evolved independently, but their derivation was dependent on regulatory networks present in a common ‘urbilaterian’ ancestor. Most strikingly, the genetic regulatory cascade comprising a key transcription factor and downstream effector genes eliciting outgrowth (such as the Drosophila melanogaster gene Distal-less or its mouse homologue Dlx) seems to have been present in such a common ancestor and has been repeatedly used to control outgrowth formation in the protostome and deuterostome lineages. Moreover, a series of deep homologies exist in the genetic systems used to pattern the appendages of vertebrates and arthropods, many of which have come to light since our original paper was written (for example, proximal-appendage specification by homo thorax in D. melanogaster or its homologue Meis1 in mice). The similarities are much more than the use of a common genetic tool kit of genes: they involve the use of genes and regulatory circuits that have previously evolved complex roles in an ancestral organism. Deep homology is important for the generation of novelties because ancient regulatory circuits provide a substrate from which novel structures can develop. In this Review, we explore three of Charles Darwin’s exemplars of evolution: animal eyes, tetrapod limbs and the giant horns of beetles. New data from studies of these features are offering surprising twists on classic examples of evolution. And, together, these examples illustrate how deep homology enables researchers to understand the generation of novelty in cases in which fossils are not informative; to make predictions about morphological transformation that can be tested by experimental and expeditionary work; and to see the extent to which common genetic mechanisms are used to generate diverse adaptations and can lead to the parallel evolution of novelties.