title: Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations.
abstract: Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first-step beneficial mutants derived from naïve and adapted genotypes used in a long-term experimental evolution of Escherichia coli. Whole-genome sequencing was able to identify the majority of beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.
authors.affiliation: Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824.
authors.forename: Marcus M
authors.initials: MM
authors.lastname: Dillon
authors.affiliation: Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824.
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Rouillard
authors.affiliation: Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824.
authors.forename: Brian
authors.initials: B
authors.lastname: Van Dam
authors.affiliation: INRA - UMR BGPI Cirad TA A-54/K, Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Gallet
authors.affiliation: Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824. vaughn.cooper@pitt.edu.|Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15219. vaughn.cooper@pitt.edu.
authors.forename: Vaughn S
authors.initials: VS
authors.lastname: Cooper
mesh_terms: D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D056084:Genetic Fitness; D058685:Genetic Pleiotropy; D005947:Glucose / Q000378:metabolism; D009154:Mutation; D012641:Selection, Genetic
chemical_list: D005947:Glucose
keywords: Adaptation; adaptive history; beneficial mutations,niche breadth; pleiotropy