Genotype networks for four example phenotypes from each of the four phenotype categories.
The four depicted networks correspond to the phenotypes plant diameter at flowering (panel A), arsenic concentration (panel C), bacterial growth (panel E), and plant width (panel G). In each network, a vertex (circle) represents a genotype (nucleotide string) and two vertices are connected by an edge if the underlying genotypes differ in one nucleotide. The size of each vertex is proportional to its vertex betweenness, which is the fraction of shortest paths through all vertex pairs that visit this vertex. Each network was laid out by the force-directed Fruchterman-Reingold graph embedding algorithm implemented in Gephi [59]. Networks shown in (A), (C) and (E) can be subdivided into two modules and each vertex in these networks is colored according to its module membership. Vertices of components that are not connected to the largest network component are colored black. Isolated vertices (that is, genotypes without a one-mutant neighbor) are not depicted. No modular structure could be detected in the genotype network of plant width (G). Box plots of panels (B), (D) and (F) show the phenotypic values in each module, where the box color is the same as that of the vertices in panels (A), (C), and (E), respectively. In each box plot, the central horizontal line indicates the median value, the lower and upper box limits correspond to first and third quartiles, whiskers indicate values within the 1.5-fold interquartile range, and each open circle shows one data point (vertex phenotype), illustrating the distribution of the phenotypic values. The number of vertices in each module is indicated as the sample size (n) on the horizontal axis. Phenotypic values differ significantly (Wilcoxon Rank-Sum Test) between genotypes in different modules of the two phenotypes plant diameter at flowering (panel B) and bacterial growth (panel F).