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identification and comparison much more difficult (Erives and Levine, 2004; Richards et al., 2005; Wittkopp, 2006) and often impossible, especially among higher arthropod taxa. To circumvent this difficulty, an alternative strategy has been to focus on rapidly evolving traits among closely related species or populations. The advantages of this approach are 2-fold: first, because the organisms under comparison diverged recently, it is expected that the number of genetic changes responsible for morphological divergence will be relatively modest and more readily distinguished from other changes not involved in morphological divergence. Second, in some cases, the relevant genetic changes can be investigated in their native ecological context and related to the potential adaptive role, if any, of morphological evolution.

Following this approach, recent studies have provided direct evidence of the role of CRE evolution in morphological evolution (Gompel et al., 2005; Jeong et al., 2006; Prud’homme et al., 2006). More importantly, these detailed functional analyses have revealed some surprising and previously unanticipated features of how gene regulation evolves at the molecular level that, we suggest, reflect general principles. The goal of this article is to articulate these emerging principles, namely how regulatory evolution: (i) proceeds using available preexisting genetic components, (ii) introduces discrete changes in gene expression thus minimizing deleterious effects and fitness penalties, and (iii) allows the association between any transcription factor and any downstream gene and thereby provides immense potential for evolutionary novelty. These principles explain both how and why regulatory sequence evolution is a pervasive, although not the exclusive, mechanism underlying morphological diversification.


Because morphological evolution is the product of the modification of the expression patterns of underlying genes, to understand how morphological changes arise, we must understand how changes in gene expression pattern arise. Pigmentation patterns in insects have been particularly amenable for these purposes for two reasons: first, many genes governing their formation have been characterized; and second, patterns are highly variable among closely related species, giving very different appearances to otherwise identical body parts (Wittkopp et al., 2003). For instance, the wings of some higher Diptera are largely identical with respect to their overall shape and venation patterns. Yet the various pigmentation patterns superimposed onto the common wing plan, ranging from a simple line, dot, or blotch to complex compound patterns make each species wing pattern largely different from the others (Fig. 6.1).

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