In principle, pigmentation patterns could evolve by changing the activity or spatial deployment of transcription factors that regulate pigmentation genes and/or by changes in the CREs of pigmentation genes themselves. Furthermore, such changes in CREs could entail either the modification of existing CREs or the de novo evolution of a CRE. Six cases of the gain or loss of pigmentation gene expression in fruit fly species have now been traced to the evolution of pigmentation gene CREs (Gompel et al., 2005; Jeong et al., 2006; Prud’homme et al., 2006). The frequency and details of CRE sequence evolution and the identity of the transcription factors involved in regulating these CREs and other case studies of morphological divergence among closely related species or populations (Belting et al., 1998; Sucena and Stern, 2000; Wang and Chamberlin, 2002; Sucena et al., 2003; Shapiro et al., 2004; Colosimo et al., 2005; Marcellini and Simpson, 2006) illustrate what we submit are general insights into the process of evolution by gene regulation.

In some members of the Drosophila melanogaster species group, the males bear dark spots at the anterior tips of their wings, whereas in most other species, they do not (Kopp and True, 2002; Prud’homme et al., 2006). The evolution of the male wing spot thus presents a simple example of a novel pattern and poses a simple question: what changed between unspotted and spotted species? The difference in pigmentation patterns is reflected by differences in pigmentation gene expression. In particular, the product of the yellow (y) gene, which is critical for the production of black pigment (Walter et al., 1991), is expressed uniformly at low levels in the developing wing blade in unspotted species and in spotted species; it is also expressed at high levels where the spot will appear.

How did yellow expression evolve? The evolutionary divergence in Yellow expression results from functional changes in a CRE controlling y expression in the developing wing (the wing CRE). In unspotted species, this CRE, which is ≈1 kb long, drives a uniform expression pattern throughout the wing (Wittkopp et al., 2002b). In spotted species, the regulatory activity of this element has changed to also drive high levels of yellow in the spot area (Gompel et al., 2005). Therefore, in this instance, an ancestral CRE has been coopted and functionally modified to become a wing + spot CRE and to generate a novel pattern.

In theory, a spot CRE with a full complement of transcription factor-binding sites necessary to drive a wing spot pattern could have evolved anywhere in the yellow locus. However, a functional CRE usually requires a substantial number of inputs to generate a spatially restricted expression