Analyses and data of:

van Houte et al. (2020) Compost spatial heterogeneity promotes evolutionary diversification of a bacterium. Journal of Evolutionary Biology

If you would like access to the paper and do not have it, please email me on d.padfield@exeter.ac.uk

DOI of paper: https://doi.org/10.1111/jeb.13722

DOI of preprint: https://doi.org/10.1101/838110

DOI of final analyses and datasets: https://doi.org/10.5281/zenodo.4155300

Link to raw sequencing files: https://www.ebi.ac.uk/ena/browser/view/PRJEB41017

Outline

This repository contains the final datasets, analyses and figures of the above-mentioned paper. It can recreate the all of the analyses and figures in the main text. The raw sequencing reads are available on ENA here.

Feedback

• Please report any problems or bugs in the code in the Issues tab of the GitHub repository. Alternatively, please email d.padfield@exeter.ac.uk.

Licensing

This code is licensed under GPL-3.

Running the scripts and analyses

• The project can be cloned or for those not familiar with GitHub, a zip file of this project can be downloaded using the "Clone or download" button at the top right of this page.
• Open the R project file in the downloaded folder. R projects automatically assigns the root directory to the directory in which the project resides. Consequently all of the analyses should be runnable without altering paths. These are very easy to open using RStudio. All of the scripts for the analyses can be found in scripts/.
• abundance_analsis.R analyses total abundance and productivity of the compost and compost-water microcosms. This script recreates Figure 1.
• resource_use_analysis.R analyses the Biolog plate assays of the evolved clones. This script recreates Figure 2.
• rel_fitness_analysis.R analyses the relative fitness of clones isolated from the compost and compost-water microcosms. This script recreates Figure 3 & Table 1.
• genomic_data_analysis.R analyses the genetic variants identified from the resequencing of the evolved clones. This script recreates Figure 4.
• calculating_resource_use_metrics.Rmd is a walk-through of how each of the metrics of functional diversity used for the Biolog plate data was calculated.
• All of the data needed to run the analyses are stored in data.
• All figures produced by the analysis are saved in figures/ and are labelled as they are in the manuscript.

All analyses are done in R version 4.0.2, on macOS High Sierra 10.13.6. I am unsure whether some older version of R will support all of the packages and whether the analyses will run exactly the same.