Evolutionary paths during network rewiring.

<p>Schematic of the intermediates we have assayed in our experiment if we assume changes in the MAD3 promoter occurred first following the gene duplication event. When the compared genotypes (nodes) are separated by a single mutational event (such as a degeneration of a functional element, which are shown as colored boxes inside the nodes), these nodes are connected by directed edges in the graph (see the example given for a loss of the first KEN box). The color of the node represents the fitness of the genotype when compared to wild-type. The color of the edge corresponds to the fitness of the descendent genotype when compared to the ancestral genotype, where red indicates a deleterious selection coefficient, black a selection coefficient with undetectable fitness effect, and green a positive selection coefficient. The color of the line representing the protein is grey for the SCP under the Bub1 promoter, yellow for the SCP under the Mad3 promoter, and black for the extant <i>S</i>. <i>cerevisiae</i> Mad3 and Bub1. Coloured boxes represent functional elements within the proteins (See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006735#pgen.1006735.g001" target="_blank">Fig 1</a> and text for details).