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.
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Chipman AD (2010) Parallel evolution of segmentation by co-option of ancestral gene regulatory networks. BioEssays 32(1):60–70CrossRefGoogle Scholar
Cotterell J, Sharpe J (2010) An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients. Mol Syst Biol 6(1)Google Scholar
Cotterell J, Robert-Moreno A, Sharpe J (2015) A local, self-organizing reaction-diffusion model can explain somite patterning in embryos. Cell Syst 1(4):257–269CrossRefGoogle Scholar
François P, Hakim V, Siggia ED (2007) Deriving structure from evolution: metazoan segmentation. Mol Syst Biol 3(1)Google Scholar
Fujimoto K, Ishihara S, Kaneko K (2008) Network evolution of body plans. PLoS One 3(7):e2772CrossRefGoogle Scholar
Graner F m c, Glazier JA (1992) Simulation of biological cell sorting using a two-dimensional extended potts model. Phys Rev Lett 69:2013–2016CrossRefGoogle Scholar
Hogeweg P (2000) Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation. J Theor Biol 203(4):317–333CrossRefGoogle Scholar
Jiménez A, Munteanu A, Sharpe J (2015) Dynamics of gene circuits shapes evolvability. PNAS 112(7):2103–2108CrossRefGoogle Scholar
Kohsokabe T, Kaneko K (2016) Evolution-development congruence in pattern formation dynamics: bifurcations in gene expression and regulation of networks structures. J Exp Zool B Mol Dev Evol 326(1):61–84CrossRefGoogle Scholar
Marin-Riera M, Brun-Usan M, Zimm R, Välikangas T, Salazar-Ciudad I (2016) Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model. Bioinformatics 32(2):219–225PubMedGoogle Scholar
Salazar-ciudad I, Jernvall J (2004) How different types of pattern formation mechanisms affect the evolution of form and development. Evol Dev 6(1):6–16CrossRefGoogle Scholar
Salazar-Ciudad I, Newman SA, Solé RV (2001) Phenotypic and dynamical transitions in model genetic networks I. Emergence of patterns and genotype-phenotype relationships. Evol Dev 3(2):84–94CrossRefGoogle Scholar
Sánchez L, Thieffry D (2003) Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J Theor Biol 224(4):517–537CrossRefGoogle Scholar
Sánchez L, Chaouiya C, Thieffry D (2008) Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. Int J Dev Biol 52:1059–1075CrossRefGoogle Scholar
Solé RV, Salazar-Ciudad I, Garcia-Fernández J (2002) Common pattern formation, modularity and phase transitions in a gene network model of morphogenesis. Physica A 305(34):640–654CrossRefGoogle Scholar
Spirov A, Holloway D (2013) Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks. Methods 62(1):39–55CrossRefGoogle Scholar
ten Tusscher K (2013) Mechanisms and constraints shaping the evolution of body plan segmentation. Eur Phys J E 36(5):1–12Google Scholar
ten Tusscher KH, Hogeweg P (2009) The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation. BMC Evol Biol 9(1):159CrossRefGoogle Scholar
ten Tusscher KH, Hogeweg P (2011) Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability. PLoS Comput Biol 7(10):e1002208CrossRefGoogle Scholar
Vroomans RMA, Hogeweg P, ten Tusscher KHWJ (2015) Segment-specific adhesion as a driver of convergent extension. PLoS Comput Biol 11(2):1–24CrossRefGoogle Scholar
Vroomans RMA, Hogeweg P, ten Tusscher KHWJ (2016) In silico evo-devo: reconstructing stages in the evolution of animal segmentation. EvoDevo 7(1):14CrossRefGoogle Scholar