Analysis scripts for "Competitive species interactions constrain abiotic adaptation in a bacterial soil community"

This record contains sample R analysis scripts associated with 'Competitive species interactions constrain abiotic adaptation in a bacterial soil community' by J. P. J. Hall et al. (2018). The data used in these analyses is presented in the Supplementary Tables published as an Excel workbook in the manuscript. For ease of analysis, .csv versions of these tables are provided in another ORDA record (doi: 10.15131/shef.data.7088906).<div><br></div><div>Full details of the experiments and their interpretation can be found in the open access paper, published in Evolution Letters (see References below). <br></div><div><br></div><div>Briefly, <i>Pseudomonas fluorescens</i> SBW25 carrying the mercury resistance plasmid pQBR57 were cultured in soil microcosms in the presence or absence of a competitor, <i>Pseudomonas putida</i> KT2440, and with or without mercury. After ~440 generations, clones were re-isolated and their fitness relative to the ancestral strain was measured. Clones from single-species treatments had increased relative fitness compared with those from co-culture. Investigation of the resequenced genomes showed parallel mutations occurring to the <i>actP</i> gene, but only in clones which had evolved without <i>P. putida</i>. Subsequent experiments show that <i>actP</i> disruption is associated with increased growth, but only where <i>P. putida</i> is absent.<div><div><div><div><br></div><div>1_CompetitionsAnalysis.R: example code describing analyses presented in Figure 1, showing relative fitness of evolved clones.</div><div><br></div><div>2_MutationsAnalysis.R: example code describing analyses presented in Figure 2, showing parallel mutations in evolved clones.</div><div><br></div><div>4_GrowthAnalysis.R: example code describing analyses presented in Figure 4, showing growth of clones with mutated and non-mutated <i>actP</i> in the presence and absence of <i>P. putida</i>.</div><div><br></div><div>S3_PopulationsAnalysis.R: example code describing analyses presented in Figure S3, showing population densities of <i>P. fluorescens</i> during evolution experiment.</div><div><br></div><div>S4_AcetateGrowth.R: example code describing analyses presented in Figure S4, showing growth of <i>P. fluorescens</i> in minimal media with glycerol or acetate as carbon sources.</div><div><br></div><div>S5A_DiscDiffusion.R: example code describing analyses presented in Figure S5A, showing inhibition of evolved <i>P. fluorescens</i> by tellurite. </div><div><br></div><div>S5B_TellMIC.R: example code describing analyses presented in Figure S5B, showing inhibition of evolved <i>P. fluorescens</i> by tellurite. </div></div><div><br></div><div><br></div></div></div></div>