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A long-standing problem in evolutionary biology is how genetic variation arises within populations and evolves to make species anatomically different. Many of the morphological differences in body plans between animal groups are thought to result from changes in gene expression during development. The rules governing the structure and evolution of cis-regulatory gene sequences are unknown, however, and the evolution of traits between closely related species remains relatively unexplored at a molecular level. To study the evolution of gene regulation, it is necessary to find a tractable trait that varies between species and for which the genetic regulation is well known in at least one of the species. The stereotyped, two-dimensional pattern of bristles on the thorax of Drosophila has been intensively investigated and is due to a precise spatial expression of proneural genes. Other species of flies have different bristle patterns and so comparisons between them provide a good paradigm for the study of changes in gene regulation. Here, we review the current state of understanding of these changes.

The origin and evolution of stereotyped patterns of macrochaetes on the nota of cyclorraphous Diptera