Modular systems consist of groups of molecules with many interactions within a group but fewer interactions between groups. Such modularity increases the chances of producing evolutionary innovations, because it allows changes inside one module without perturbing others, and because it permits redeployment of modules to create new biological functions. We simulate the evolution of gene networks known to be important in development to show that modularity increases when selection favors specialization in gene activity. Specialization occurs wherever new cell types, organs, or other body structures arise. In the course of this process gene networks acquire the ability to produce new gene activity patterns specific to these structures. We also demonstrate how modularity favors the evolution of new gene activity patterns that make use of already existing modules. Because specialization in gene activity is very common in evolution, the mechanism that we put forward may be important for the origins of modularity in gene regulatory networks.

Transcriptional and posttranslational control are two major mechanisms of eukaryotic gene regulation. Transcriptional and posttranslational regulatory interactions assemble into networks which share many global topological properties with each other and with regulatory networks in general. Given the highly distinct nature of transcriptional and posttranslational regulation at the molecular scale, we address the question how and at which organizational level the similarity between both types of regulation emerges.