Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

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Cryptic variation is caused by the robustness of phenotypes to mutations1. Cryptic variation has no effect on phenotypes in a given genetic or environmental background, but it can have effects after mutations or environmental change2, 3, 4, 5. Because evolutionary adaptation by natural selection requires phenotypic variation, phenotypically revealed cryptic genetic variation may facilitate evolutionary adaptation6, 7, 8. This is possible if the cryptic variation happens to be pre-adapted, or “exapted”9, to a new environment, and is thus advantageous once revealed. However, this facilitating role for cryptic variation has not been proven, partly because most pertinent work focuses on complex phenotypes of whole organisms whose genetic basis is incompletely understood. Here we show that populations of RNA enzymes with accumulated cryptic variation adapt more rapidly to a new substrate than a population without cryptic variation. A detailed analysis of our evolving RNA populations in genotype space shows that cryptic variation allows a population to explore new genotypes that become adaptive only in a new environment. Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution10, 11.

At a glance


  1. Evolution during selection for the native activity.
    Figure 1: Evolution during selection for the native activity.

    a, Activity (fraction of ribozyme reacted) at each generation under conditions used during selection for the native activity (RNA oligonucleotide cleavage) over 10 generations (Methods). Error bars correspond to standard errors of three measurements. b, c, Histograms, from each generation of line A and B, showing the frequency (percent of sample) of individuals with a given number of nucleotide differences from the wild-type sequence (distance). Frequencies from generations 1 (G1) and 10 (G10) are shown as solid lines, and intervening generations are shown as dotted grey lines.

  2. Evolution during selection for the new activity.
    Figure 2: Evolution during selection for the new activity.

    a, Activity (fraction of ribozyme reacted) at each generation under conditions used during selection for phosphorothioate bond cleavage, with standard error based on three measurements. b, Frequency of genotypes (percent of sample) over time (generations), and their corresponding relative fitness w. c, Comparison of kinetic parameters for the Azo* and wild-type ribozymes. d, Intermolecular activity of the AzoΔ ribozyme, under the same conditions as during selection (Methods): 200pmol phosphorothioate substrate, 20pmol 5′-[32P]-labelled AzoΔ. In addition, lanes 3 and 4 contained 40pmol wild-type and Azo*, respectively. The negative control ‘No S’ contained no substrate.

  3. Evolution in genotype space.
    Figure 3: Evolution in genotype space.

    a, Principal component analysis of pooled sequence data from New-A, New-B and New-WT populations. The first two principal components are shown (‘PC1’ and ‘PC2’). Nodes represent individual sequences. The distance between nodes is proportional to the number of nucleotide differences, but may appear decreased due to the compression of multiple dimensions. The region on the graphs occupied by the AzoΔ sequences is indicated by a grey ellipse. bd, Frequency of sequences with a given number of the Azo* mutations in generation 10 of line B (B10, b), and the first generation of line New-WT (New-WT1, c) and line New-B (New-B1, d). Frequencies are presented as percentage (left y-axis) and total number (right y-axis).


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  1. Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland

    • Eric J. Hayden,
    • Evandro Ferrada &
    • Andreas Wagner
  2. The Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland

    • Eric J. Hayden,
    • Evandro Ferrada &
    • Andreas Wagner
  3. The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA

    • Andreas Wagner


E.J.H. and A.W. contributed to the design of the experiments; E.J.H. performed the experiments; E.J.H., E.F., and A.W. all contributed to analysis of the data and co-wrote the paper.

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