Questioning the Ubiquity of Neofunctionalization
Figure 8
The effect of gene duplication on the clustering coefficient.
Every connected network containing three to nine nodes was enumerated producing 273,191 networks containing 2,445,434 nodes. (A) Changes to the clustering coefficient resulting from simple duplication and homomeric duplication. Each of the 2,445,434 nodes was duplicated twice, once as self-interacting (homomeric) and once as non-self-interacting (simple). Shown is the change in clustering coefficient for each duplication, ordered by magnitude. The enumerated networks serve as possible subnetworks of larger protein interaction networks. The magnitude of the vertical axis is determined by the size of the network, but the shape of the curves around zero remains unchanged. (B) The severe effect subfunctionalization has on the clustering coefficient. The vertical axis represents the portion of the 2,445,434 gene duplications in the enumerated networks which result in a decrease in the clustering coefficient. Probability of Loss is the probability the gene duplicate (progeny) loses each of its interactions due to subfunctionalization. Even without losses suffered due to subfunctionalization, simple duplications reduce the clustering coefficient in over 76% of examined duplications. By contrast, clustering coefficients produced via homomeric duplication are far more likely to increase even in the face of interaction losses caused by subfunctionalization. (C) The effect of subfunctionalization on aggregate ΔC. The change in clustering coefficient aggregated for all 2,445,434 duplications at each loss probability. While aggregate ΔC of simple duplication is below zero for all loss probabilities, homomeric duplications remain above zero until the Probability of Loss≈0.62.