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The Reproducibility of Adaptation in the Light of Experimental Evolution with Whole Genome Sequencing

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Book cover Ecological Genomics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 781))

Abstract

A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests some shortcomings of the reductionist approach. We conclude that convergence may be better defined at an integrated level, such as the genic level or even at a phenotypic level, and that integrated mechanistic models derived from systems biology may offer an interesting perspective for the analysis of convergence at all levels.

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Acknowledgments

This work was supported by grants from the Agence Nationale de la Recherche (Grant ANR-12-JSV7-0007-01 to G.A., Grant ANR-08-GENM-023-001 to O.T.) and NSF grant DEB-0748903 to BS.G and A.RV.

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Authors and Affiliations

  1. UMR7148 and Atelier de Bioinformatique, UPMC, Paris, France

    Guillaume Achaz

  2. CIRB, Collège de France, Paris, France

    Guillaume Achaz

  3. INSERM, UMR-S 722, Paris, 75018, France

    Alejandra Rodriguez-Verdugo & Olivier Tenaillon

  4. University Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Site Xavier Bichat, Paris, 75018, France

    Alejandra Rodriguez-Verdugo & Olivier Tenaillon

  5. Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA

    Alejandra Rodriguez-Verdugo & Brandon S. Gaut

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  1. Guillaume Achaz
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  2. Alejandra Rodriguez-Verdugo
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  3. Brandon S. Gaut
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  4. Olivier Tenaillon
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Correspondence to Olivier Tenaillon .

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Editors and Affiliations

  1. Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Quebec, Québec, Canada

    Christian R. Landry

  2. Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Quebec, Québec, Canada

    Nadia Aubin-Horth

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Achaz, G., Rodriguez-Verdugo, A., Gaut, B.S., Tenaillon, O. (2014). The Reproducibility of Adaptation in the Light of Experimental Evolution with Whole Genome Sequencing. In: Landry, C., Aubin-Horth, N. (eds) Ecological Genomics. Advances in Experimental Medicine and Biology, vol 781. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7347-9_11

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