Title

Codes for: A numerical model supports the evolutionary advantage of recombination plasticity in shifting environments

Authors

• Sviatoslav R. Rybnikov
• Sariel Hübner
• Abraham B. Korol

2. Codes/Data Description

File structure

The folder contains:

• input file "regimes.txt"
• five script files for GNU Octave v. 8.1.0 ("*.m")
• file "results.xlsx" with results of the main simulations

INPUT FILE

The input file "regimes.txt" contains characteristics of 1,000 selection regimes analyzed in the study. Each row describes a specific regime, including:

• half-period T (column 1);
• selection intensity s (column 2);
• dominance lift d (column 3);
• the lower and the upper values of recombination compatible with polymorphism maintenance in the selected system (columns 4 and 5).

SCRIPTS

The scripts must be launched sequentially since they generate output files needed for the next scripts, as follows:

1. Script "1_find_optima.m" estimates the optimal constant recombination r* for each selection regime from input file "regimes.txt". The found optima will appear in an intermediate output file optima.txt. The estimated calculation time is ~45 h (for Intel® Core™ i7-7700K CPU @ 4.20GHz, RAM 8 GB).
2. Script "2_split_optima.m" analyses the found optima (the intermediate output file optima.txt), finds those that had converged, and splits them into two or three groups:
   • with r*=0 (output file "optima_zero.txt");
   • with r*=0.5 (output file "optima_free.txt");
   • [if exist] with r* between 0 and 0.5 (output file "optima_int.txt");
3. Scripts "3_test_plastic_vs_zero.m", "4_test_plastic_vs_free.m" and "5_test_plastic_vs_int.m" compare plastic recombination vs r*=0, r*=0.5, and r* between 0 and 0.5, respectively. The results of these comparisons will appear in the main output files: plastic_vs_zero.txt (~8 h), plastic_vs_free.txt (~5 h), and plastic_vs_int.txt (~0.5 h)

Output files

The main output files are "plastic_vs_zero.txt", "plastic_vs_free.txt" and "plastic_vs_int.txt". Each line in these files corresponds to a specific selection regime and contains the following information:

• half-period T (column 1);
• selection intensity s (column 2);
• dominance lift d (column 3);
• the optimal constant recombination r* (column 4);
• comparison between the optimal constant recombination r* (allele M1) and one-generation plastic recombination with the magnitude Δr=0.025 (allele M2) – columns 5-14;
• comparison between the optimal constant recombination r* (allele M1) and one-generation plastic recombination with the magnitude Δr=0.05 (allele M2) – columns 15-24;
• comparison between the optimal constant recombination r* (allele M1) and one-generation plastic recombination with the magnitude Δr=0.1 (allele M2) – columns 25-34;
• comparison between the optimal constant recombination r* (allele M1) and damped transgenerational plastic recombination with the magnitude Δr=0.05 (allele M2) – columns 35-44;
• comparison between the optimal constant recombination r* (allele M1) and non-damped transgenerational plastic recombination with the magnitude Δr=0.05 (allele M2) – columns 45-54.

Each comparison (i.e., columns 5-14, 15-24, 25-34, 35-44 and 45-54) contains the following information:

• geometric mean and range of fitness under allele M1 at the beginning of the burn-in stage – e.g., columns 15-16 for one-generation plastic recombination with Δr=0.05;
• geometric mean and range of fitness under allele M1 at the end of the burn-in stage – e.g., columns 17-18 for one-generation plastic recombination with Δr=0.05;
• geometric mean and range of fitness under allele M2 at the beginning of the burn-in stage – e.g., columns 19-20 for one-generation plastic recombination with Δr=0.5;
• geometric mean and range of fitness under allele M2 at the end of the burn-in stage – e.g., columns 21-22 for one-generation plastic recombination with Δr=0.5;
• the increases in frequency of allele M2 from initial frequencies of 0.05 and 0.95 – e.g., columns 23-24 for one-generation plastic recombination with Δr=0.5.

IMPORTANT!

Scripts "1_find_optima.m", "3_test_plastic_vs_zero.m", "4_test_plastic_vs_free.m", and "5_test_plastic_vs_int.m" by default assume panmixia and linked modifier. To perform simulations for partial selfing, change the parameter slf (line 24) in the mentioned scripts from 0 to 0.1 or 0.2. To perform simulations for unlinked modifier, change the parameter linkM (line 58) in the mentioned scripts from 0.2 to 0.5.

CAUTION!!!

All scripts clean the existing output files before simulations. Thus, before changing parameters slf and/or linkM, care to copy the scripts into a new folder in order not to lose the results of previous simulations.

Simulation results

File "results.xlsx" contains results of the basic simulations, i.e. those implying:

• panmixia
• one-generation shift-inducible recombination
• magnitude of the plastic increase Δr=0.05

The file contains four sets of simulated data:

• linked modifier, regimes with r*=0 (sheet 1)
• linked modifier, regimes with r*=0.5 (sheet 2)
• unlinked modifier, regimes with r*=0 (sheet 3)
• unlinked modifier, regimes with r*=0.5 (sheet 4)

Each sheet contains the following variables:

• half-period T column A)
• selection intensity s (column B)
• selection intensity expressed as 1/sigma^2 (column C)
• cumulative selection expressed as Ts (column D)
• cumulative selection expressed as T/sigma^2 (column E)
• geometric mean of population mean fitness (column F)
• range of population mean fitness (column G)
• advantage of shift-inducible recombination over the optimal constant recombination (1 - yes, 0 - no) (column H)

3. Sharing/Access Information

License: CC0 1.0

4. Version History

Starting from version 6:

• all script files are annotated
• file "results.xlsx" with results of basic simulations is included