Rapid evolution of the functionally conserved gap genegiantinDrosophila

Developmental processes in multicellular organisms, and the outcomes they produce, are often evolutionarily conserved. Yet phylogenetic conservation of developmental outcomes is not reflected in functional preservation of the genes regulating these processes, a phenomenon referred to as developmental system drift (1, 2). Little is known about the evolutionary forces producing change in the molecular details of regulatory genes and their networks while preserving development outcomes. Here we address this void in knowledge by systematically swapping the Drosophila melanogaster coding and noncoding regions of the essential gap gene, giant , a key regulator of embryonic pattern formation, with orthologous sequences drawn from both closely and distantly related species within the genus. Employing sensitized genetic complementation assays, the loss of a transgene’s ability to restore viability occurs across phylogeny at every interspecific level of comparison and includes both coding and noncoding changes. Epistasis is present as well — both between coding and noncoding sequences and, in a dramatic example of change-of-sign epistasis, between the only two coding substitutions separating two very closely related species. A continuous process of functional divergence hidden under conserved phylotypic developmental outcomes requires reconsideration of the prevailing view that the essential genes in conserved regulatory networks are protected from the driving forces of evolutionary change.