Selection and constraint on regulatory elements in Drosophila simulans

We utilized available Drosophila simulans molecular population genomic data to characterize sequence polymorphism in noncoding regulatory regions and their corresponding transcribed target genes or interacting transcription factors. We highlight two properties of regulatory evolution. First, we find that sequence divergence between D. melanogaster and D. simulans is greater at regulatory sites than expected from levels of intraspecific polymorphism, suggestive of positive selection. Second, we compared variation in cis-regulatory regions to that of the transcription factors and transcribed target genes with which they are associated. We find a correlation in polymorphism between cis-regulatory regions and the transcription factors which they bind, but not between cis-regulatory regions and the physically neighboring target genes which they directly regulate. This result indicates that the evolution of cis-regulatory elements is constrained by the interactions among transcription factors and regulatory regions. More broadly, these findings support the general importance of noncoding regulatory DNA in evolution.