Reconstructing the evolution of molecular interaction networks under the DMC and link dynamics models

Abstract

Molecular interaction networks have emerged as a powerful data source for answering a plethora of biological questions ranging from how cells make decisions to how species evolve. The availability of such data from multiple organisms allows for their analysis from an evolutionary perspective. Indeed, work has emerged recently on network alignment, ancestral network reconstruction, and phylogenetic inference based on networks. In this paper, we address two central issues in the area of evolutionary analysis of molecular interaction networks, namely (1) correcting genetic distances derived from observed differences between networks, and (2) reconstructing ancestral networks from extant ones. We address both issues computationally under the link dynamics and duplication-mutation with complementarity (DMC) evolutionary models. We demonstrate the utility and accuracy of our methods on biological and simulated data. © 2012 Springer-Verlag.