Modeling Evolution of Developmental Gene Regulatory Networks

The field of evo-devo studies what, how, and why developmental patterning processes have evolved. While comparative approaches based in experimental data are essential for answering the first two types of questions, evo-devo simulations studies are critical to answer why questions. By simulating evo-devo processes, the evolutionary tape can be replayed both under the same and different conditions, enabling us to answer questions on contingency, convergence, and constraints and their roles in determining evolutionary outcomes. In this chapter, we describe the basic ingredients of computational models simulating evo-devo processes: gene expression regulation; cell and tissue behavior; and mutation-selection driven evolution. We describe for each of these model ingredients the choices that need to be made, e.g., whether the model simulates a one, two, or three-dimensional tissue, and how these affect computational efficiency as well as modeling outcomes. We focus on the importance of incorporating a realistic, nonlinear, and evolvable genotype-phenotype map in evo-devo simulation models. We end with an illustration of how evo-devo models have helped answer why questions in the field of animal body plan segmentation