DOI: 10.5061/dryad.62s22
title: Data from: Genomic evolution of bacterial populations under co-selection by antibiotics and phage

description: Bacteria live in dynamic systems where selection pressures can alter
 rapidly, forcing adaptation to the prevailing conditions. In particular,
 bacteriophages and antibiotics of anthropogenic origin are major bacterial
 stressors in many environments. We previously observed that populations of
 the bacterium Pseudomonas fluorescens SBW25 exposed to the lytic
 bacteriophage SBW25Φ2 and a non-inhibitive concentration of the antibiotic
 streptomycin (co-selection) achieved higher levels of phage resistance
 compared to populations exposed to the phage alone. In addition, the phage
 became extinct under co-selection while remaining present in the phage
 alone environment. Further, phenotypic tests indicated that these
 observations might be associated with increased mutation rate under
 co-selection. In this study, we examined the genetic causes behind these
 phenotypes by whole-genome sequencing clones isolated from the end of the
 experiments. We were able to identify genetic factors likely responsible
 for streptomycin resistance, phage resistance and hypermutable (mutator)
 phenotypes. This constitutes genomic evidence in support of the
 observation that while the presence of phage did not affect antibiotic
 resistance, the presence of antibiotic affected phage resistance. We had
 previously hypothesized an association between mutators and elevated
 levels of phage resistance under co-selection. However, our evidence
 regarding the mechanism was inconclusive, since although with phage
 mutators were only found under co-selection, additional genomic evidence
 was lacking and phage resistance was also observed in non-mutators under
 co-selection. More generally, our study provides novel insights into
 evolution between univariate and multivariate selection (here two
 stressors), as well as the potential role of hypermutability in natural
 communities.
description: Quality-filtered VCF
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