Here is the third chapter of “Origins of Evolutionary Innovations”! This chapter describes innovations in regulatory systems, and the evolution of networks of transcription factor sites.
The most important message of this chapter is that regulatory circuits can suffer a lot of changes, and yet remain functional. For example, some researchers have change up to 600 transcription factors in E.coli, yet it was still able to survive. Or, as another nice example, galactose metabolism is regulated by two completely different transcription factors in S.cerevisiae and C.albicans, yet these two species are not so distant philogenetically.
Another important message of this chapter is the structure of genotype networks of metabolic circuit. I think it can be well represented by this figure taken from [1]. It represents that, in order to find new phenotypes, a genotype network must be robust to changes (all the possible genotypes must be connected), but also be large, so it is able to explore the genotype space.
[1]Ciliberti, S., Martin, O., & Wagner, A. (2007). Innovation and robustness in complex regulatory gene networks Proceedings of the National Academy of Sciences, 104 (34), 13591-13596 DOI: 10.1073/pnas.0705396104