11 The Reproducibility of Adaptation in the Light of Experimental Evolution with Whole Genome Sequencing Guillaume Achaz, Alejandra Rodriguez-Verdugo, Brandon S. Gaut, and Olivier Tenaillon 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 prop- erties of the adaptive landscape. Reductionist approaches have high- lighted 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 G. Achaz UMR7148 and Atelier de Bioinformatique, UPMC, Paris, France CIRB, Collège de France, Paris, France A. Rodriguez-Verdugo INSERM, UMR-S 722, Paris 75018, France University Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Site Xavier Bichat, Paris 75018, France Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA O. Tenaillon () INSERM, UMR-S 722, Paris 75018, France University Paris Diderot, Sorbonne Paris Cité, UMR-S 722, Site Xavier Bichat, Paris 75018, France e-mail: olivier.tenaillon@inserm.fr B.S. Gaut Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697, USA C.R. Landry and N. Aubin-Horth (eds.), Ecological Genomics: Ecology and the Evolution of Genes and Genomes, Advances in Experimental Medicine and Biology 781, DOI 10.1007/978-94-007-7347-9__11, © Springer ScienceCBusiness Media Dordrecht 2014 211