Evolutionary history of regulators and regulatory interactions. (a) Most of the transcription factors (TFs) regulate adjacent genes. These 'neighbor regulators' are often transferred between related bacteria and are often lost, and so they seem to be niche specific. Neighbor regulated genes are often regulated by other regulators as well, but this regulation is usually not conserved across horizontal gene transfer (HGT) events. (b) Scenarios for the evolution of regulatory interactions. For each scenario, we show the proportion of known regulatory interactions in E. coli  that evolved that way. Scenario 1: regulatory interactions are conserved after gene duplication in a small fraction of cases. Scenario 2: even when paralogous TFs or paralogous regulated genes have similar regulatory interactions, this often results from the evolution of similar regulation after HGT, rather than being conserved from the duplication event. Scenario 3: in some cases, a single region of DNA evolves to bind two paralogous TFs. Unlike scenario 2, this scenario relies on the similarity of the TFs. Scenario 4: Most TFs, and probably most other genes as well, ultimately arose by a duplication, either within a lineage or by allopatric gene divergence. Nevertheless, the regulatory interactions are usually not shared with their paralogs. (To estimate a frequency for scenario 4, we assumed that all genes arose by some kind of duplication.) Separate results for paralogous TFs, for paralogous regulated genes, and for paralogs of both are given in Table 1.