Fig. 1

Overview of the model. a Simulation of gene expression phenotypes. We show a simple TRN with one TF (yellow) and one effector gene (blue), with arrows for major biological processes simulated in the model. b Phenotype–fitness relationship. Fitness is primarily determined by the concentration of an effector protein (here shown as beneficial as in Eq. 4, but potentially deleterious in a different environment as in Eq. 5), with a secondary component coming from the cost of gene expression (proportional to the rate of protein production), combined to give an instantaneous fitness at each moment in gene expression time. c Evolutionary simulation. A single resident genotype is replaced when a mutant’s estimated fitness is high enough. Stochastic gene expression adds uncertainty to the estimated fitness, allowing less fit mutants to occasionally replace the resident, capturing the flavor of genetic drift