Asymptotic Evolution of Protein-Protein Interaction Networks for General Duplication-Divergence Models

TL;DR

This paper presents an asymptotic analysis of a general duplication-divergence model for protein-protein interaction networks, revealing conditions that lead to conserved, scale-free network structures relevant to biology.

Contribution

It introduces a new asymptotic solution for a general duplication-divergence model and defines a conservation index to quantify network evolutionary conservation.

Findings

Conserved, non-dense networks are necessary for biological relevance.

Scale-free networks emerge under specific microscopic parameter conditions.

The model links microscopic duplication-divergence processes to global network topology.

Abstract

Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary process must have largely conditioned the emerging structure of protein-protein interaction (PPI) networks, that control many cellular activities. We propose and asymptotically solve a general duplication-divergence model of PPI network evolution based on the statistical selection of duplication-derived interactions. We also introduce a conservation index, that formally defines the statistical evolutionary conservation of PPI networks. Distinct conditions on microscopic parameters are then shown to control global conservation and topology of emerging PPI networks. In particular, conserved, non-dense networks, which are the only ones of potential biological relevance, are also shown to be necessary scale-free.