Modularity "for free" in genome architecture?

Abstract

Background: Recent models of genome-proteome evolution have shown that some of the key traits displayed by the global structure of cellular networks might be a natural result of a duplication-diversification (DD) process. One of the consequences of such evolution is the emergence of a small world architecture together with a scale-free distribution of interactions. Here we show that the domain of parameter space were such structure emerges is related to a phase transition phenomenon. At this transition point, modular architecture spontaneously emerges as a byproduct of the DD process. Results: Although the DD models lack any functionality and are thus free from meeting functional constraints, they show the observed features displayed by the real proteome maps when tuned close to a sharp transition point separating a highly connected graph from a disconnected system. Close to such boundary, the maps are shown to display scale-free hierarchical organization, behave as small worlds and exhibit modularity. Conclusions: It is conjectured that natural selection tuned the average connectivity in such a way that the network reaches a sparse graph of connections. One consequence of such scenario is that the scaling laws and the essential ingredients for building a modular net emerge for free close to such transition.