Dataset DOI: 10.5061/dryad.fqz612k4h

Description of the data and file structure

There are two main types of data, all described in detail below. 

1) Python code used to generate all the data used in the article, ending .ipynb or .py. 

• DataMerger.py
• AnalyzeClusterData.ipynb
• MatingWormsCluster.ipynb
• PlottingClusterData.ipynb
• WormFunctionsMating.py
• FitnessFigures.ipynb
• ScanningXi.ipynb
• ShowExtinction.ipynb

2) Simulated data in .npy format, readable by Python. 

• CombinedDataL2.zip (114.34 MB)
• CombinedDataL6.zip (876.47 MB)

Code:

The Python code was written in Python 3 in Jupyter Notebook. 

Necessary packages: sys, numpy, matplotlib and WormFunctionsMating.py

WormFunctionsMating.py

This is the main file containing all the classes (e.g. Experiment, Population) that are necessary to run the simulations. This file needs to be placed in the same directory as the following file MatingWormsCluster[2].ipynb for simulations to be run. 

MatingWormsCluster.ipynb and MatingWormsCluster2Loci.ipynb

These are the two files that can run simulations for situations with 6 and 2 loci, respectively, by calling functions defined in WormFunctionsMating.py. They define the parameters of the individual experiment and call the necessary functions to run it: all details of the experiments are encoded here. Individual outputs of the simulations are saved in individual files.
Data saved are time courses of population sizes of male and hermaphrodite subpopulations, concentrations, dilutions and mutant frequencies. Generations are also saved in files. 

DataMerger.py

This code merges batches of individual output data repeats (generated by MatingWormsCluster.ipynb ) together for future manipulation. Repeats that should be merged together are defined within the file by specifying the parameters of the experiment for which the merging is performed.

The files are saved as
name+’N’+(N)+’L’+(L)+’E’+(E)+’X’+(X)+’D’+(D)+’all’+(data name)
where
name is your desired name preposition
N is the population size
L is the number of loci
E is epistasis
X is the fraction of mating hermaphrodites
D is dominance.

These variables uniquely define a simulated scenario. Data name describes type of data saved:

frequency (allele frequency of individual mutations),
dilutions (needed to restore populations to the original size),
time (generation count),
concentration (concentration at which the worms were surviving at a given time), dynamics_h (population sizes of hermaphrodites)
dynamics_m (population sizes of males).

For your convenience, data outputs from DataMerger.py are provided in this depository, as described below.
The following scripts use data generated by DataMerger.py for calculations and plotting. 

AnalyzeDataCluster.ipynb

This code takes the outputs of DataMerger.py and calculates and plots relevant statistics and observations.

ScanningXi.ipynb

This script loads data created by DataMerger and analyses the effect of the fraction of hermaphrodites on the drug concentration that worms adapted to. It creates figures saved as ‘FigFirstToFixVaryXL’+(L)+’D’+(D)+’NAll.png’ where L is the number of loci (2 or 6) and D is dominance (0 for recessive and 1 for dominant).

FitnessFigures.ipynb

This is a script that allows plotting fitness figures based on the experiment parameters, defined within the file.

ShowExtinctions.ipynb

This script allows for the reproduction of preliminary simulations testing the extinction and survival of worms at various concentrations, depending on the steepness of the concentration increase.

Data

CombinedData2.zip contains simulation data for two-loci scenarios
CombinedData6.zip contains simulation data for six-loci scenarios

These data are outputs of DataMerger.py, which merges outputs from individual repeats together for easier manipulation. These data can be directly used by AnalyzeDataCluster.ipynb and ScanningXi.ipynb for analysis, to produce figures shown in the manuscript.

Name convention is as follows:
WormsT500+‘N’+(N)+’L’+(L)+’E’+(E)+’X’+(X)+’D’+(D)+’all_’+(data name)*
where

N is the population size (200, 2000, 20 000 or 200 000)
L is the number of loci (2 or 6)
E is epistasis (0 in all simulated cases)
X is the fraction of mating hermaphrodites (range from 0 to 1 in 0.1 increments)
D is dominance (0 for recessive mutation, 1 for dominant mutation).

These variables uniquely define a simulated scenario, and the files contain all the repeats for the respective scenario. The following data are included:

frequency (allele frequency of individual mutations),
dilutions (needed to restore populations to the original size),
time (generation count),
concentration (concentration at which the worms were surviving at a given time), dynamics_h (population sizes of hermaphrodites)
dynamics_m (population sizes of males).

Sharing/Access information

The code is also available at: https://github.com/Trubenova/MatingSystemCelegans