title: Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli.
abstract: Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment (LTEE) with Escherichia coli have also diversified extensively in nature. To make this comparison, we identified ∼2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to modify protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to its evolutionary history in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.
authors.affiliation: Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI.|BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI.|Department of Systems Biology, Harvard Medical School, Boston, MA.
authors.forename: Rohan
authors.initials: R
authors.lastname: Maddamsetti
authors.affiliation: Department of Computer Science, University of New Hampshire, Durham, NH.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Hatcher
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA.
authors.forename: Anna G
authors.initials: AG
authors.lastname: Green
authors.affiliation: Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI.
authors.forename: Barry L
authors.initials: BL
authors.lastname: Williams
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA.
authors.forename: Debora S
authors.initials: DS
authors.lastname: Marks
authors.affiliation: Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI.|BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Lenski
keywords: core genome; experimental evolution; fine-tuning mutations; loss-of-function mutations; molecular evolution