A major, and sometimes heated, debate in evolutionary and developmental biology is about the genetic basis of morphological evolution and the molecular mechanisms of gene regulatory evolution. Central to this argument is whether gene regulation most often evolves from changes in the cis-regulatory elements of genes or through changes in the transcription factors that bind to regulatory elements. Although various kinds of theoretical and experimental evidence have been used to advance the cause of both sides, none has been more influential than the finding that transcription factors from very different organisms can be functionally conserved. In this perspective, we review the now classic finding that Pax6 genes from flies and vertebrates are functionally conserved in eye development and can induce the formation of eyes when swapped between species. While a conserved role for Pax6 genes in eye development is undebatable, we show that evidence of divergent Pax6 functions has been overlooked and propose that Pax6 genes have evolved novel protein functions during the development of the Drosophila eye, coincident with the evolution of a novel eye developmental mechanism in cyclorrhaphan dipterans. Thus, we conclude that Pax6 genes are both functionally equivalent and divergent between species.
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