Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

Gustavo Caetano-Anolles, M. Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés

Research output: Contribution to journalReview article

Abstract

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.

Original languageEnglish (US)
JournalEvolutionary Bioinformatics
Volume15
DOIs
StatePublished - Jan 1 2019

Fingerprint

Metabolomics
Metabolic Networks and Pathways
Transcriptome
Proteins
protein
metabolomics
Growth
Metabolism
transcriptome
linkage (genetics)
proteins
metabolism
timescale
Biological Sciences
Protein Domains
analysis

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications

Cite this

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. / Caetano-Anolles, Gustavo; Aziz, M. Fayez; Mughal, Fizza; Gräter, Frauke; Koç, Ibrahim; Caetano-Anollés, Kelsey; Caetano-Anollés, Derek.

In: Evolutionary Bioinformatics, Vol. 15, 01.01.2019.

Research output: Contribution to journalReview article

Caetano-Anolles, Gustavo ; Aziz, M. Fayez ; Mughal, Fizza ; Gräter, Frauke ; Koç, Ibrahim ; Caetano-Anollés, Kelsey ; Caetano-Anollés, Derek. / Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. In: Evolutionary Bioinformatics. 2019 ; Vol. 15.
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