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Evolutionary changes in transcription networks are an important source of diversity across species, yet the quantitative consequences of network evolution have rarely been studied. Here we consider the transcriptional ‘rewiring’ of the three  GAL  genes that encode the enzymes needed for cells to convert galactose to glucose. In  Saccharomyces cerevisiae , the transcriptional regulator Gal4 binds and activates these genes. In the human pathogen  Candida albicans  (which last shared a common ancestor with  S. cerevisiae  some 300 million years ago), we show that different regulators, Rtg1 and Rtg3, activate the three  GAL  genes. Using single-cell dynamics and RNA-sequencing, we demonstrate that although the overall logic of regulation is the same in both species—the  GAL  genes are induced by galactose—there are major differences in both the quantitative response of these genes to galactose and in the position of these genes in the overall transcription network structure of the two species.

Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression