title: Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.
abstract: Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.
authors.affiliation: Ecology, Evolutionary Biology, and Behavior Program, Michigan State University BEACON Center for the Study of Evolution in Action, Michigan State University maddamse@msu.edu.
authors.forename: Rohan
authors.initials: R
authors.lastname: Maddamsetti
authors.affiliation: Department of Computer Science, University of New Hampshire.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Hatcher
authors.affiliation: CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.affiliation: CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.affiliation: BEACON Center for the Study of Evolution in Action, Michigan State University Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin.
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
authors.affiliation: Ecology, Evolutionary Biology, and Behavior Program, Michigan State University BEACON Center for the Study of Evolution in Action, Michigan State University.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Lenski
mesh_terms: D005075:Biological Evolution; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D023281:Genomics; D059645:Mutation Rate; D010802:Phylogeny; D012641:Selection, Genetic; D000069456:Silent Mutation
keywords: effective population size; experimental evolution; genetic variation; mutation rate