Experimental evolution of a pathogen confronted with innate immune memory increases variation in virulence

R Markdown file and Data for Manuscript: Experimental evolution of a pathogen confronted with innate immune memory increases variation in virulenceAuthors: Ana Korša , Moritz Baur, Nora Schulz, Jaime M. Anaya-Rojas , Alexander Mellmann, Joachim Kurtz

The data here are listed in the order they are used in the manuscript for figures and analysisAbbreviations: P-primed evolved pathogen, C-control evolved pathogen, A-ancestral pathogen

By using data below and the script provided within a Markdown file, one could recreate the analysis. 

Additionally, the script and data used for Bayesian analysis is provided separately. 

1)Proportion mortality - data set with the proportion of mortality (virulence in host per individual bacterial replicate used for Figure 12)Selection mortality - data set used for statistical analysis. 0- represents alive host, 1- dead host3)Spore load data - xls.data set used for spore load plot 4)Spore load data - csv file used for statistical analysis 5)Sporeload_mortality_spores_fitness - file used for spore growth analysis and plot. It is also used for plotting and analysis of fitness measures It combines proportion mortality data, average spore growth data/replicate, and fitness measure and correlation analysis in supplements6)average_proportion_priming_sensitivity_fitness - data set used for plotting and analysis of priming sensitivity and correlation of priming sensitivity and fitness7)2023-08Btt-cry-qPCR-results.csv - data set used for Cry gene expression analysis and plot8)Final variants - data set used for genomic variants heatmap9)plasmids - data set used for analysis and plotting the plasmids 10)plasmids_cry - data set used for correlation of cry expression and 188kn plasmid 11)Phage_log2diff - Phage coverage shown as log2 difference whole chromosome and phage coverage used for plots and analysis12)Pearson global - file used for correlation matrix in the supplements. Combines spore growth, spore load, virulence, cry expression, 188 kb plasmids, and 3 phages to see if there are some significant correlations in primed and control evolved pathogen13) Pearson's new data set is used for the correlation matrix in the supplements. It combines priming sensitivity, fitness, Cry expression, phages, and a 188kb plasmid. 

Bayesian analysis - Main. R, analysis. R, data and data_priming : details are explained in Read_me file.