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Evol Bioinform Online. 2019 Sep 5;15:1176934319872980. doi: 10.1177/1176934319872980. eCollection 2019.

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.

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Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, C.R. Woese Institute for Genomic Biology, and Illinois Informatics Institute, University of Illinois, Urbana, IL, USA.
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Turkey.
Division of Biomedical Informatics, College of Medicine, Seoul National University, Seoul, Republic of Korea.
European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.


Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies and the other that diversifies. Here, we propose a biphasic (bow-tie) theory of module emergence. In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels. Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism, elementary functionomes, and protein domain organization.


Accretion; biphasic bow-tie pattern; evolutionary diversification; molecular structure; phylogenomic analysis; ribosome

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Declaration of Conflicting Interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

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