Erwin, Douglas H. 2020. "Evolutionary dynamics of gene regulation." In Gene Regulatory Networks. Peter, I. S., editor. 407–431. London, England: Academic Press Limited-Elsevier Science Limited. In Current Topics in Developmental Biology, 139. https://doi.org/10.1016/bs.ctdb.2020.02.006.
The long controversy over the importance of changes in the regulatory genome has been resolved with the recognition that such changes are a fundamental component of evolutionary dynamics. Comparative studies have revealed four dominant modes of change as the regulatory genome evolved: (1) the origin of regulatory novelties such as distal enhancers and new types of promoters at the origin of Metazoa; (2) the expansion of regulatory capacity, most notably with diversification of transcription factors. Together these changes expanded the available combinatoric complexity of regulatory interactions and allow an increase in the variety of cell types. There are two more common modes of regulatory evolution: (3) Repatterning of gene regulatory networks. Such repatterning largely involves the introduction of transposons, promoter switching, co-option of regulatory genes or subcircuits, recombination, and the de novo generation of new regulatory sequences. Finally, (4) changes in enhancer and promoter specificity enable fine-scale adaptive changes. One of the outstanding issues at the intersection of evolutionary and developmental biology is how these various modes of regulatory evolution translate to morphological change, and particularly macro- and microevolutionary patterns and whether evolutionary novelties are associated with distinctive patterns of regulatory change.
