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Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein

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  • Andreas Wagner

    (University of Zurich
    Quartier Sorge-Batiment Genopode
    The Santa Fe Institute)

Abstract

Can evolvability—the ability to produce adaptive heritable variation—itself evolve through adaptive Darwinian evolution? If so, then Darwinian evolution may help create the conditions that enable Darwinian evolution. Here I propose a framework that is suitable to address this question with available experimental data on adaptive landscapes. I introduce the notion of an evolvability-enhancing mutation, which increases the likelihood that subsequent mutations in an evolving organism, protein, or RNA molecule are adaptive. I search for such mutations in the experimentally characterized and combinatorially complete fitness landscapes of a protein and an RNA molecule. I find that such evolvability-enhancing mutations indeed exist. They constitute a small fraction of all mutations, which shift the distribution of fitness effects of subsequent mutations towards less deleterious mutations, and increase the incidence of beneficial mutations. Evolving populations which experience such mutations can evolve significantly higher fitness. The study of evolvability-enhancing mutations opens many avenues of investigation into the evolution of evolvability.

Suggested Citation

  • Andreas Wagner, 2023. "Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39321-8
    DOI: 10.1038/s41467-023-39321-8
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    1. Adam C. Palmer & Erdal Toprak & Michael Baym & Seungsoo Kim & Adrian Veres & Shimon Bershtein & Roy Kishony, 2015. "Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
    2. Gregory I. Lang & Daniel P. Rice & Mark J. Hickman & Erica Sodergren & George M. Weinstock & David Botstein & Michael M. Desai, 2013. "Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations," Nature, Nature, vol. 500(7464), pages 571-574, August.
    3. Júlia Domingo & Guillaume Diss & Ben Lehner, 2018. "Pairwise and higher-order genetic interactions during the evolution of a tRNA," Nature, Nature, vol. 558(7708), pages 117-121, June.
    4. Frank J. Poelwijk & Michael Socolich & Rama Ranganathan, 2019. "Learning the pattern of epistasis linking genotype and phenotype in a protein," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    5. Xianghua Li & Jasna Lalić & Pablo Baeza-Centurion & Riddhiman Dhar & Ben Lehner, 2019. "Author Correction: Changes in gene expression predictably shift and switch genetic interactions," Nature Communications, Nature, vol. 10(1), pages 1-1, December.
    6. Xianghua Li & Jasna Lalić & Pablo Baeza-Centurion & Riddhiman Dhar & Ben Lehner, 2019. "Changes in gene expression predictably shift and switch genetic interactions," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
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