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Data from: Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection

Citation

Card, Kyle J.; LaBar, Thomas; Gomez, Jasper B.; Lenski, Richard E. (2019), Data from: Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection, v3, Dryad, Dataset, https://doi.org/10.5061/dryad.g41hg96

Abstract

Populations often encounter changed environments that remove selection for the maintenance of particular phenotypic traits. The resulting genetic decay of those traits under relaxed selection reduces an organism’s fitness in its prior environment. However, whether and how such decay alters the subsequent evolvability of a population upon restoration of selection for a previously diminished trait is not well understood. We addressed this question using Escherichia coli strains from the long-term evolution experiment (LTEE) that independently evolved for multiple decades in the absence of antibiotics. We first confirmed that these derived strains are typically more sensitive to various antibiotics than their common ancestor. We then subjected the ancestral and derived strains to various concentrations of these drugs to examine their potential to evolve increased resistance. We found that evolvability was idiosyncratic with respect to initial genotype; that is, the derived strains did not generally compensate for their greater susceptibility by “catching up” to the resistance level of the ancestor. Instead, the capacity to evolve increased resistance was constrained in some backgrounds, implying that evolvability depended upon prior mutations in a historically contingent fashion. We further subjected a time-series of clones from one LTEE population to tetracycline and determined that an evolutionary constraint arose early in that population, corroborating the role of contingency. In summary, relaxed selection not only can drive populations to increased antibiotic susceptibility, but it can also affect the subsequent evolvability of antibiotic resistance in an unpredictable manner. This conclusion has potential implications for public health, and it underscores the need to consider the genetic context of pathogens when designing drug-treatment strategies.

Methods

The data were collected using plate-based evolvability and fluctuation assays that are described in detail in the associated publication. All of the statistical analyses of experimental data were performed using the R software environment (version 3.5.0). The details of our statistical analyses are provided in the associated R Notebook titled "Historical contingency in the evolution of ABR". This Notebook was written using RStudio (version 1.2.1181).

Usage Notes

The data package associated with the paper "Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection" contains two zip folders:


1.  Card et al. (2019) - Data and R notebook


File:  Historical contingency in the evolution of ABR.Rmd (and .html)

This R notebook contains code to analyze all data and generate all figures associated with the paper. A .html file is also included for convienence so one may examine the analysis outputs without running the code. 
 

Folder:  Figures

This folder contains Figs 2, 3, and 4 that output from the R Notebook.
 

File:  MICs of LTEE ancestral and derived strains.csv

This is the data file for the minimum inhibitory concentrations (MICs) of various antibiotics on the LTEE ancestor and derived clones isolated from generation 50,000 populations, and their resistant mutant derivatives.


File:  MICs of strains from Ara+5 population.csv

This is the data file for the minimum inhibitory concentrations (MICs) of tetracycline on the LTEE ancestor and derived clones isolated from the Ara+5 population, and their resistant mutant derivatives.
 

File:  Cell counts.csv

This is the data file for the estimated cell yields among twelve replicate populations of the LTEE ancestor and a derived clone isolated from the Ara+5 population after 2,000 generations.
 

File:  Mutant colony counts.csv

This is the data file for tetracycline resistant mutant colony counts of the LTEE ancestor and a derived clone isolated from the Ara+5 population after 2,000 generations.

 

2.  Card et al. (2019) - Experimental plate photos

This zip folder contains photos of all experimental plates for our evolvability assays.

Funding

National Science Foundation, Award: DEB-1451740

National Science Foundation, Award: DBI-0939454

References