The evolution of Bab paralog expression and abdominal pigmentation among Sophophora fruit fly species.

The evolution of gene networks lies at the heart of understanding trait divergence. Intrinsic to development is the dimension of time: a network must be altered during the correct phase of development to generate the appropriate phenotype. One model of developmental network evolution is the origination of dimorphic (male-specific) abdomen pigmentation in the fruit fly subgenus Sophophora. In Drosophila (D.) melanogaster, dimorphic pigmentation is controlled by the dimorphic expression of the paralogous Bab1 and Bab2 transcription factors that repress pigmentation. These expression patterns are thought to have evolved from a monomorphic ancestral state. Here we show that the spatial domain and contrast in dimorphic Bab expression increases during the latter half of pupal development, and this late pupal expression is necessary and sufficient to suppress pigmentation. Late pupal Bab expression was monomorphic for species from basal clades exhibiting monomorphic pigmentation, though dimorphic expression was observed in D. pseudoobscura that represents an intermediate-branching monomorphic clade. Among species from the dimorphic Sophophora clades, Bab expression was dimorphic, but a poor correlation was found between the domains of expression and male pigmentation. Lastly, while Bab paralog co-expression was generally observed, an instance of paralog-specific expression was found, indicating more complex regulatory mechanisms and mutational effects have shaped the evolution of the bab locus. These results highlight the importance of the time and place of Bab expression for pigmentation development and evolution, and suggest that dimorphism evolved early in Sophophora, but diversity in male pigmentation was not further shaped by alterations in Bab expression.

Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation diversity.

The development of morphological traits occurs through the collective action of networks of genes connected at the level of gene expression. As any node in a network may be a target of evolutionary change, the recurrent targeting of the same node would indicate that the path of evolution is biased for the relevant trait and network. Although examples of parallel evolution have implicated recurrent modification of the same gene and cis-regulatory element (CRE), little is known about the mutational and molecular paths of parallel CRE evolution. In Drosophila melanogaster fruit flies, the Bric-à-brac (Bab) transcription factors control the development of a suite of sexually dimorphic traits on the posterior abdomen. Female-specific Bab expression is regulated by the dimorphic element, a CRE that possesses direct inputs from body plan (ABD-B) and sex-determination (DSX) transcription factors. Here, we find that the recurrent evolutionary modification of this CRE underlies both intraspecific and interspecific variation in female pigmentation in the melanogaster species group. By reconstructing the sequence and regulatory activity of the ancestral Drosophila melanogaster dimorphic element, we demonstrate that a handful of mutations were sufficient to create independent CRE alleles with differing activities. Moreover, intraspecific and interspecific dimorphic element evolution proceeded with little to no alterations to the known body plan and sex-determination regulatory linkages. Collectively, our findings represent an example where the paths of evolution appear biased to a specific CRE, and drastic changes in function were accompanied by deep conservation of key regulatory linkages.