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Dynamical community structure of populations evolving on genotype networks

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  • Capitán, José A.
  • Aguirre, Jacobo
  • Manrubia, Susanna

Abstract

Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics.

Suggested Citation

  • Capitán, José A. & Aguirre, Jacobo & Manrubia, Susanna, 2015. "Dynamical community structure of populations evolving on genotype networks," Chaos, Solitons & Fractals, Elsevier, vol. 72(C), pages 99-106.
    • Handle: RePEc:eee:chsofr:v:72:y:2015:i:c:p:99-106
    DOI: 10.1016/j.chaos.2014.11.019
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    1. Jesús Gómez-Gardeñes & Gorka Zamora-López & Yamir Moreno & Alex Arenas, 2010. "From Modular to Centralized Organization of Synchronization in Functional Areas of the Cat Cerebral Cortex," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-11, August.
    2. Diego Prada-Gracia & Jesús Gómez-Gardeñes & Pablo Echenique & Fernando Falo, 2009. "Exploring the Free Energy Landscape: From Dynamics to Networks and Back," PLOS Computational Biology, Public Library of Science, vol. 5(6), pages 1-9, June.
    3. Eric van Nimwegen & James P. Crutchfield & Martijn Huynen, 1999. "Neutral Evolution of Mutational Robustness," Working Papers 99-03-021, Santa Fe Institute.
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