Monochromaticity in neutral evolutionary network models.

Recent studies on epistatic networks of model organisms have unveiled a certain type of modular property called monochromaticity in which the networks are clustered into functional modules that interact with each other through the same type of epistasis. Here, we propose and study three epistatic network models that are inspired by the duplication-divergence mechanism to gain insight into the evolutionary basis of monochromaticity and to test if it can be explained as the outcome of a neutral evolutionary hypothesis. We show that the epistatic networks formed by these stochastic evolutionary models have monochromaticity conflict distributions that are centered close to zero and are statistically significantly different from their randomized counterparts. In particular, the last model we propose yields a strictly monochromatic solution. Our results agree with the monochromaticity findings in real organisms and point toward the possible role of a neutral mechanism in the evolution of this phenomenon.

[1]  S. Redner,et al.  Infinite-order percolation and giant fluctuations in a protein interaction network. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  A. Wagner How the global structure of protein interaction networks evolves , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[3]  R. Tsien,et al.  Specificity and Stability in Topology of Protein Networks , 2022 .

[4]  E. Ziv,et al.  Information-theoretic approach to network modularity. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[5]  Cheng-Yan Kao,et al.  A quantitative analysis of monochromaticity in genetic interaction networks , 2011, BMC Bioinformatics.

[6]  Santo Fortunato,et al.  Community detection in graphs , 2009, ArXiv.

[7]  I. Ispolatov,et al.  Duplication-divergence model of protein interaction network. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[8]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[9]  M. Cosentino Lagomarsino,et al.  Hierarchy and feedback in the evolution of the Escherichia coli transcription network , 2007, Proceedings of the National Academy of Sciences.

[10]  G. Church,et al.  Modular epistasis in yeast metabolism , 2005, Nature Genetics.

[11]  Kim Sneppen,et al.  Physics in molecular biology , 2005 .

[12]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[13]  Trey Ideker,et al.  Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data , 2008, PLoS Comput. Biol..

[14]  Gary D Bader,et al.  The Genetic Landscape of a Cell , 2010, Science.

[15]  G. Wagner,et al.  The road to modularity , 2007, Nature Reviews Genetics.

[16]  Dr. Susumu Ohno Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[18]  P. Bourgine,et al.  Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.

[19]  Gary D Bader,et al.  Quantitative analysis of fitness and genetic interactions in yeast on a genome scale , 2010, Nature Methods.

[20]  P. Phillips Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems , 2008, Nature Reviews Genetics.

[21]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[22]  Victor H Hernandez,et al.  Nature Methods , 2007 .

[23]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[24]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[25]  Ricard V. Solé,et al.  A Model of Large-Scale proteome Evolution , 2002, Adv. Complex Syst..

[26]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[27]  Nature Genetics , 1991, Nature.

[28]  Stefan Bornholdt,et al.  Less Is More in Modeling Large Genetic Networks , 2005, Science.

[29]  P. Pin,et al.  Assessing the relevance of node features for network structure , 2008, Proceedings of the National Academy of Sciences.

[30]  Fergal P. Casey,et al.  Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs , 2011, BMC Systems Biology.

[31]  R. Solé,et al.  Spontaneous emergence of modularity in cellular networks , 2008, Journal of The Royal Society Interface.

[32]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

[33]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[34]  R. Albert Scale-free networks in cell biology , 2005, Journal of Cell Science.

[35]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[36]  A. Vespignani,et al.  Modeling of Protein Interaction Networks , 2001, Complexus.