General set-up

We extend an existing individual based model of a population of organisms evolving on a lattice [26] (Fig. 1a). Each organism possesses a so-called pearls-on-a-string genome consisting of genes encoding transcription factors (TFs) and upstream regulatory regions with transcription factor binding sites (TFBS) [28]. At birth, organisms consist of a short one-dimensional row of cells which grows through the course of the individual’s development. An individual’s probability of reproduction (fitness) depends on the number of segments present in its gene expression pattern after a predefined amount of developmental time.

Overview of the model. a The developing individuals live on a 2D lattice. Each individual consists of a row of cells. The genome of the individual codes for a network of regulatory interactions, which determines the spatio-temporal dynamics of the proteins within each cell (see d). b The initial conditions for each new individual at the start of its development. There are a growth zone with high morphogen and a ‘head’ region without morphogen. The morphogen dynamics may vary. Either they are imposed, yielding persistent posterior morphogen (left) the morphogen is kept at a high level in the posterior-most cell while decaying in the other cells, or the morphogen can become regulated by the network, so that only the initial conditions are specified (right). c Divisions are regulated by a division protein; when its level passes a threshold, the cell can divide. Upon division, the level of the division protein in both daughter cells is halved, but not the level of the other proteins. d At the end of development, the expression of the segmentation gene is averaged over a number of time steps, and from this the segment boundaries are determined. e The mutational operators acting on the genome