title: Specificity of genome evolution in experimental populations ofEscherichia colievolved at different temperatures.
abstract: Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations ofEscherichia coliwere evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily alternations between 32 °C and 42 °C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated ∼5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited ∼17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only ∼4%. For example, all six strains evolved at 32 °C had mutations innadR, whereas none of the other 24 strains did. However, a population evolved at 37 °C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when tested in the others, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments.
authors.affiliation: Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712.|Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712.|Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.|Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Deatherage
authors.affiliation: Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712.|Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712.|Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.|Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.
authors.forename: Jamie L
authors.initials: JL
authors.lastname: Kepner
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697.
authors.forename: Albert F
authors.initials: AF
authors.lastname: Bennett
authors.affiliation: BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824; jbarrick@cm.utexas.edu lenski@msu.edu.|Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Lenski
authors.affiliation: Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712; jbarrick@cm.utexas.edu lenski@msu.edu.|Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712.|Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712.|Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.|BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824.
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D019020:Directed Molecular Evolution; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D056084:Genetic Fitness; D016680:Genome, Bacterial / Q000235:genetics; D009154:Mutation; D010641:Phenotype; D012641:Selection, Genetic; D013696:Temperature
keywords: experimental evolution; genome evolution; mutation; natural selection; temperature