Network motifs of three (a) and four (b) genes found in the transcriptional network of A. thaliana. Here we plot the most statistically significant motifs (see Additional data file 2 for a complete list of motifs). (c) The FFL, a motif significantly overrepresented, where an external factor inhibits gene A thereby limiting expression of gene B, but this is compensated for by indirect regulation through gene C. (d) The evolution of the qualitative development of a plant with motifs (dashed line) and without motifs (solid line) under changing environments. We note that there is an evolutionary optimization, including topological units such as FFLs, that provides robustness under external factors despite decreasing system fitness (areas I and II) due to excess expression of those genes providing indirect interactions. (e) Distribution of normalized robustness coefficients (ρ*) computed for all interactions between TFs and genes.