Reverse engineering the evolution of protein interaction networks.

Protein interaction network analyses have moved beyond simple topological observations to functional and evolutionary inferences based on the construction of putative ancestral networks. Evolutionary studies of protein interaction networks are generally derived from network comparisons, are limited in scope, or are theoretic dynamic models that aren't contextualized to an organism's specific genes. A biologically faithful network evolution reconstruction which ties evolution of the network itself to the actual genes of an organism would help fill in the evolutionary gaps between the gene network "snapshots" of evolution we have from different species today. Here we present a novel framework for reverse engineering the evolution of protein interaction networks of extant species using phylogenetic gene trees and protein interaction data. We applied the framework to Saccharomyces cerevisiae data and present topological trends in the evolutionary lineage of yeast.