Materials for Resource Abundance and the Critical Transition to Cooperation

This repository contains data, configuration files, and analysis scripts related to Resource Abundance and the Critical Transition to Cooperation. To ensure reproducibility, Avida version 2.12.4, which was used for this work, is also included. Protocols used for the microbial experiments are described in the paper.

Contents

• analysis - Scripts for analyzing and plotting result data
• avida - Source code for Avida 2.12.4
• configuration - Configuration files for reported simulations
• data - Result data sets
• figures - Figures

Contents by Figure

Figure	Data File(s)	Analysis
1	N/A	N/A
2	(a) data/cooperators.csv.bz2 (b) data/eps.csv.bz2 (c) data/kills.csv.bz2 (d) data/popsizes.csv.bz2, data/popsizes_noEPS.csv.bz2	analysis/plot_avida_combined.R
3	(a) data/coop_cheats_r010_411.csv (b) data/coop_cheats_r030_411.csv	analysis/plot_avida_popstacks.R
4	data/fluctuation_treatments.csv, data/fluctuation_cooppct.csv	analysis/plot_avida_fluctuation.R
5	data/vc_wt_7d_biofilm.csv	analysis/plot_vc_biofilm.R
6	data/vc_frac_rugose.csv	analysis/plot_vc_rugose.R
7	(a) data/vc_evolved_absorbance.csv (b) data/vc_comp_initial.csv, data/vc_comp_planktonic_24h.csv, data/vc_comp_biofilm_24h.csv (c) data/EvolvedVibrioCholeraeBiofilmYieldsCfu2_051716.csv	analysis/plot_vc_evolved_all.R
S1	data/data/population_spatial_r30.csv.bz2	analysis/plot_avida_population.R
S2	data/cooperators.csv.bz2	analysis/plot_avida_coop_trajectories.R
S3	data/reactions.csv.bz2	analysis/plot_avida_EQU.R
S4	data/vc_WT_growth.csv	analysis/plot_vc_growth.R
Video S1	data/population_spatial_r30.csv.bz2	analysis/make_population_video.R

Funding

This work was supported in part by National Science Foundation grants CNS-1059373, CNS-0915855, DBI-0939454, CCF-0820220, CNS-0751155, DBI-1309318; and National Institutes of Health grants R01-GM109259 and R01-GM110444.

License

Data, configuration files, and figures are released under a Creative Commons Attribution 4.0 International License (CC BY 4.0). Analysis code is released under the MIT license. Avida is released under the GNU Lesser General Public License.