Figure 2

A simple example of network evolution. (a) At the regulatory level, gene 4 receives inputs from genes 1 and 2 in the ancestral state (inputs to genes 1, 2 and 3 not shown). A hypothetical protein expression pattern for this system is also shown (b). Following duplication and degeneration, regulatory subfunctionalization arises for gene 4 (dotted interactions are lost). A new input from gene 3 means we additionally have neofunctionalization, i.e., subneofunctionalization. After further degeneration (a, right) regulatory subfunctionalization is lost, while neofunctionalization is retained. (c) All three post-duplication states (sub-, subneo-, neo-functionalization) will result in temporal subfunctionalization for gene 4, since in the second and third timesteps only the first copy (u₄) is ON, whereas in the fifth and sixth timesteps only the second copy (v₄) is ON.