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An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus

Nature Genetics volume 37, pages 441–444 (2005)Cite this article

Abstract

The primary impediment to formulating a general theory for adaptive evolution has been the unknown distribution of fitness effects for new beneficial mutations1. By applying extreme value theory2, Gillespie circumvented this issue in his mutational landscape model for the adaptation of DNA sequences3,4,5, and Orr recently extended Gillespie's model1,6, generating testable predictions regarding the course of adaptive evolution. Here we provide the first empirical examination of this model, using a single-stranded DNA bacteriophage related to φX174, and find that our data are consistent with Orr's predictions, provided that the model is adjusted to incorporate mutation bias. Orr's work suggests that there may be generalities in adaptive molecular evolution that transcend the biological details of a system, but we show that for the model to be useful as a predictive or inferential tool, some adjustments for the biology of the system will be necessary.

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Figure 1: A schematic depiction of the extreme value theory predictions for a single step.
Figure 2: A comparison of the observed data with the expectations under Orr's model and the mutation-adjusted models.

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Acknowledgements

We thank J.J. Bull, Z. Abdo, H.A. Orr and L. Wahl for discussions and comments. This work was supported by a grant from the US National Institutes of Health.

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Author notes

  1. S Brian Caudle

    Present address: Department of Biological Sciences, Section of Integrative Biology, University of Texas, Austin, Texas, 78712, USA

Authors and Affiliations

  1. Department of Biological Sciences, University of Idaho, Moscow, 83844, Idaho, USA

    Darin R Rokyta, S Brian Caudle & Holly A Wichman

  2. Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, 83844, Idaho, USA

    Darin R Rokyta, Paul Joyce & Holly A Wichman

  3. Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, 83844, Idaho, USA

    Darin R Rokyta, Paul Joyce & Holly A Wichman

  4. Department of Mathematics, University of Idaho, Moscow, 83844, Idaho, USA

    Paul Joyce

  5. Department of Statistics, University of Idaho, Moscow, 83844, Idaho, USA

    Paul Joyce

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  1. Darin R Rokyta
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Corresponding author

Correspondence to Holly A Wichman.

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Rokyta, D., Joyce, P., Caudle, S. et al. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet 37, 441–444 (2005). https://doi.org/10.1038/ng1535

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