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Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

Citation

Zwart, Mark P. et al. (2022), Data from: Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution, Dryad, Dataset, https://doi.org/10.5061/dryad.b2rbnzsh2

Abstract

The study "Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution" by Schenk et al. explores the phenotypic and genotypic changes in Escherichia coli after 500 generations of laboratory adaptation to increasing concentrations of an antibiotic (CTX). The source data files and scripts pertaining to the figures in the main manuscript and the extended data are available on the publishers webiste. Here we provide the source data files and scripts pertaining to the supplementary materials, organized according the figures in the supplementary material. Data are provided for Figures S2-S4, S6-S8, and S10-S12.

Methods

We characterized evolved clones and populations with different methods, with both phenotypic and genotypic characterization.

Antibiotic resistance was determined with minimal inhibitory concentration (MIC) assays, but we also measured their beta-lactamase activity with nitrocefin assays. The competitive fitness of selected mutations was determined by competitions with flourescently marked strains, followed by flow cytometry.

Illumina sequencing was performed on a randomly selected clone from each evolved population. In addition, we sequenced meta-populations from 5 large and 5 small populations at 100, 200, 300, 400 and 500 generations. Raw sequencing data are available in the Sequencing Read Arhive (PRJNA790633), of the NCBI. Mutations were called from the sequencing data using different methods, and the set of mutations was manually curated to remove any sequencing or mapping artefacts. The set of mutations was used for subsequent analyses, such as determining the occurence of mutations in different classes, the repeatability of evolution, and the co-occurence of adaptive mutations.

Usage Notes

An overview of the data files provided and how they are organized is given in ReadMe.rtf

To make the submission coherent and complete, we have included a PDF of the supplementary materials (Supplementary Materials Schenk Zwart et al Nature Ecology and Evolution.pdf).