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pattern (Davidson, 2001). If a functional CRE were to evolve from naïve DNA, the evolutionary path to acquire all of the necessary transcription factor-binding sites, in a functional arrangement, would be relatively long, and it is difficult to see how selection might favor the intermediates. In contrast, a CRE that is functional in a given tissue already contains some of the sites necessary to direct gene expression in that tissue, and therefore it represents a more likely template to accommodate a new expression pattern in that tissue, because a relatively shorter evolutionary path would lead to functional novelty. Consequently, it seems more probable that a novel gene expression pattern in a tissue will arise from random mutations creating binding sites in the vicinity of an existing CRE driving expression in that tissue than from mutations in non-functional DNA.

Which trans-acting factor-binding sites have evolved in the wing CRE to create the spot pattern? In principle, this element could have evolved binding sites for a single transcriptional activator, which, in turn, had evolved to be expressed in a spot pattern. In fact, however, the formation of the yellow spot pattern entailed the evolution of binding sites for both activators and repressors involved in the building of the wing. In particular, the transcription factor Engrailed, present in cells in the posterior part of the wing, directly represses yellow expression, confining elevated yellow expression and, therefore, the formation of the pigmentation spot to the anterior region (Gompel et al., 2005).

The key point regarding the identity of Engrailed is that it is not a transcription factor specifically dedicated to pigmentation. Engrailed is a deeply conserved component of arthropod segmentation and appendage development, and its expression in the posterior compartment long preceded its involvement in the patterning of the pigmentation spot (Patel et al., 1989). Nevertheless, in this particular context, the evolutionary process took advantage of its presence and established a direct regulatory connection between Engrailed and a pigmentation gene, thus sculpting the contour of the pigmentation spot. In this instance, Engrailed has been recruited for a new function, without any change occurring in its activity, protein sequence, or expression.

The evolution of the wing spot illuminates a general mechanism by which a novel pigmentation pattern can be generated (Fig. 6.2). The development of the wing or any body part or organ is a sequential process controlled by an array of regulatory proteins (Carroll et al., 2004). As development proceeds, the expression of these proteins progressively delineates the wing layout, position of the veins, sensory organs, and so on. Collectively, the expression profiles of all wing-building transcription factors compose a complex mosaic of superimposed patterns or “trans-regulatory landscape” (Fig. 6.3). If and when combinations of binding sites for members of the trans-regulatory landscape evolve in the CRE of

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