title: You cannot tell a book by looking at the cover: Cryptic complexity in bacterial evolution.
abstract: Do genetically closely related organisms under identical, but strong selection pressure converge to a common resistant genotype or will they diverge to different genomic solutions? This question gets at the heart of how rough is the fitness landscape in the local vicinity of two closely related strains under stress. We chose a Growth Advantage in Stationary Phase (GASP) E scherichia coli strain to address this question because the GASP strain has very similar fitness to the wild-type (WT) strain in the absence of metabolic stress but in the presence of metabolic stress continues to divide and does not enter into stationary phase. We find that under strong antibiotic selection pressure by the fluoroquinolone antibiotic ciprofloxacin in a complex ecology that the GASP strain rapidly evolves in under 20 h missense mutation in gyrA only 2 amino acids removed from the WT strain indicating a convergent solution, yet does not evolve the other 3 mutations of the WT strain. Further the GASP strain evolves a prophage e14 excision which completely inhibits biofilm formation in the mutant strain, revealing the hidden complexity of E. coli evolution to antibiotics as a function of selection pressure. We conclude that there is a cryptic roughness to fitness landscapes in the absence of stress.
authors.affiliation: Department of Physics, University of Illinois , Urbana-Champaign, Urbana, Illinois 61801, USA.
authors.forename: Qiucen
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Physics, Princeton University , Princeton, New Jersey 08544, USA.
authors.forename: Julia
authors.initials: J
authors.lastname: Bos
authors.affiliation: Department of Physics, Princeton University , Princeton, New Jersey 08544, USA.
authors.forename: Grigory
authors.initials: G
authors.lastname: Tarnopolskiy
authors.affiliation: Department of Electrical Engineering, Princeton University , Princeton, New Jersey 08544, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Sturm
authors.affiliation: Genome Sequencing Center, University of California , Santa Cruz, California 95064, USA.
authors.forename: Hyunsung
authors.initials: H
authors.lastname: Kim
authors.affiliation: Genome Sequencing Center, University of California , Santa Cruz, California 95064, USA.
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
authors.affiliation: Department of Physics, Princeton University , Princeton, New Jersey 08544, USA.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Austin