Comparative Analysis of Modularity in Biological Systems

In systems biology, comparative analysis of molecular interactions across diverse species indicates that conservation and divergence of networks can be used to understand functional evolution from a systems perspective. A key characteristic of these networks is their modularity, which contributes significantly to their robustness, as well as adaptability. In this paper, we investigate the evolution of modularity in biological networks through phylogenetic analysis of network modules. Namely, we develop a computational framework, which identifies modules in networks of diverse species independently and projects these modules into the networks of other species, with a view to capturing the evolutionary trajectories of functional modules. These trajectories can then be used to reconstruct modular phylogenies and whole-network phylogenies, or to enhance identification of functional modules. In the context of phylogeny reconstruction, our experiments on a comprehensive collection of simulated and real networks show that comparison of networks based on module trajectories is more informative than other measures of network similarity. These results demonstrate the key role of modularity in the functional evolution of biological systems and motivate further investigation of the evolution of functional modules.