This repository contains the necessary scripts and files to run all simulations in the manuscript and plot all figures

unzip PPEL_scripts_plotting_data.zip to get access to all files described below

To plot figures, use Polyploid_expansion_load.Rproj which will allow the use of all plotting scripts in plotting_expansion_load.r using relative paths to the Rproject folder without needing to change locally

Data for plotting are stored in simdata/* folder. Within *sim_data/, the basic/ folder contains simulations for generating Figures 1-4 which are simulations that don’t include diploidization in the main text. burnin/ contains the data generated for testing the burnin period. low_mig/ contains simulation data for lower migration rates where m is set to 0.005. dip/ contains all of the main diploidization simulation data and can be used to generate Figures 5-6. no_PAFC/ contains diploidization simulation data where pairing associated fitness costs are removed.

The SLiM_scripts/ folder contains each script and supporting files to run the simulations. the src/ folder contains necessary model functions for processing simulation data and running the simulations in model_functions.slim. output_reg.slim contains the processing code to create the output files for the basic, non-diploidization simulations. output_dip_dom.slim contains the processing code to create the output files for the diploidization meiotic gene model scripts. output_dip.slim contains the processing code to create the output files for the diploidization by pairing efficiency.

For using the main SLiM scripts in SLiM_scripts/ : polyploid_expansion.slim, polyploid_diploidization_dominant_meiotic.slim, and polyploid_diploidization_pairing_efficiency.slim, follow the instructions below:

SLiM simulator for polyploid expansion load study. All sims were run using SLiM v 4.0.1 https://messerlab.org/slim/

For keyword parameters, the following are accepted:

NOTE: for the paper, bd_dr is used for the recessive model as deleterious are recessive and beneficial are dominant

Diploidization only:

To run each of the scripts, the following will work as examples

slim -d "out_dir='out'" -d g_size=999999 -d K=100 -d "r=log(2)" -d mig_rate=0.05 -d u_del=2.5e-8 -d u_ben=2.5e-9 -d b_s=0.005 -d d_s=-0.005 -d rho=2.5e-8 -d "inheritance='auto'" -d "dom_pattern='bd_dr'" -d "s_dist='gamma'" polyploid_expansion.slim 

For the diploidization scripts, if using the meiotic gene model run the following script:

slim -d "out_dir='out'" -d g_size=999999 -d K=100 -d "r=log(2)" -d dip_lambda=2 -d rho=2.5e-8 -d remove_dip_muts=1 -d mig_rate=0.05 -d u_del=2.5e-8 -d u_ben=2.5e-9 -d u_dip=2.5e-10 -d b_s=0.05 -d d_s=-0.005 -d "dom_pattern='auto'" -d "dip_model='dom'" polyploid_diploidization_dominant_meiotic.slim

and for the pairing efficiency model:

slim -d "out_dir='out'" -d g_size=999999 -d K=100 -d "r=log(2)" -d dip_lambda=100 -d rho=2.5e-8 -d remove_dip_muts=1 -d meiotic_fitness=1 -d mig_rate=0.05 -d u_del=2.5e-8 -d u_ben=2.5e-9 -d u_dip=2e-3 -d b_s=0.005 -d d_s=-0.005 -d "dom_pattern='bd_dr'" -d "dip_model='diff'" -d pe_inflection=85 -d pe_slope=1 -d "s_dist='gamma'" polyploid_diploidization_pairing_efficiency.slim

for diploidization, the extra parameter ‘remove_dip_muts’ governs whether diploidization mutations are removed prior to expansion (1 is yes, 0 no), and for the pairing efficiency model, ‘meiotic fitness’ regulates if pairing associate fitness effects are included (PAFCs; 1 for yes, 0 for no), pe_inflection is the inflection point of the model (𝛽), and pe_slope is the slope parameter of the model (𝛿).

For a single population, an example script has been added to the slim_extras repository https://github.com/MesserLab/SLiM-Extras/blob/master/models/autotetraploid.slim