Gene regulatory networks are generally thought to be made up of a few highly connected nodes (hubs) and many poorly connected nodes nested within a hierarchical regulatory regime. Thus gene regulatory networks approximate a hierarchical scale free network topology. This is consistent with the view that most genes have limited pleiotropy and operate within regulatory modules. This structure is thought to evolve due to the preferential attachment of duplicated genes to more highly connected genes. Recent work has also shown that natural selection tends to favor networks with sparse connectivity.
There are primarily two ways that networks can evolve, both of which can occur simultaneously. The first is that network topology can be changed by the addition or subtraction of nodes (genes) or parts of the network (modules) may be expressed in different contexts. The Drosophila Hippo signaling pathway provides a good example. The Hippo signaling pathway controls both mitotic growth and post-mitotic cellular differentiation. Recently it was found that the network the Hippo signaling pathway operates in differs between these two functions which in turn changes the behavior of the Hippo signaling pathway. This suggests that the Hippo signaling pathway operates as a conserved regulatory module that can be used for multiple functions depending on context. Thus, changing network topology can allow a conserved module to serve multiple functions and alter the final output of the network. The second way networks can evolve is by changing the strength of interactions between nodes, such as how strongly a transcription factor may bind to a cis-regulatory element. Such variation in strength of network edges has been shown to underlie between species variation in vulva cell fate patterning of Caenorhabditis worms.