<p>(A) Evolution in <i>cis</i> alone, for example via binding site gain, can require only a single evolutionary step. Solid versus dashed lines/shapes represent different species. Binding sites (black) and transcription factors (gray) interact in the same way in both species, but a binding site (star) has been gained in the donor's <i>cis</i>-regulatory element, recruiting an existing regulator into the gene regulatory network. An enhancer swap combines this <i>cis</i> element (in needle) with the <i>trans</i> environment of the host (in circle), which is sufficient to drive a donor-like pattern. Divergence in <i>trans</i> alone is also possible, but is not depicted here. (B) <i>cis-trans</i> coevolution leads to misregulation upon swap. Binding sites and transcription factors interact in different ways in the two species. The donor <i>cis</i> element lacks the information that the host <i>trans</i> factors need to drive proper expression, so the pattern is not interpreted correctly. Not all <i>cis-trans</i> coevolution will take place through divergence of transcription factors and their binding sites as depicted; interactions with co-factors, the distribution of factors, etc. can also cause divergence in <i>trans</i> to a given enhancer (not shown).</p
