Predicting the invasiveness of underdominance gene drives

This repository contains all code needed to reproduce results from the forthcoming paper, "Predicting the invasiveness of underdominance gene drives".

SLiM models

• 1D:
  • oneD-diffusion-model.slim is for underdominance alleles and homing underdominance gene drives.
  • oneD-diffusion-model-tade.slim is for TADE modification and suppression drives.
• 2D:
  • twoD-diffusion-model.slim is for underdominance alleles and homing underdominance gene drives.
  • twoD-diffusion-model-tade.slim is for TADE modification and suppression drives.

See the SLiM model README for details on running these models.

Reaction-diffusion simulations using deSolve

• The critical release width (in 1D) or diameter (in 2D) based on deSolve simulations can be found numerically using the find_critical_rde_release_stat function in prediction-functions.R. It relies on code from:

  • underdominance-functions.R
  • homing-gd-functions.R
  • tade-modification-functions.R
  • tade-suppression-functions.R

• The phat threshold for TADE modification or suppression can also be found numerically using the find_phat_tade function in prediction-functions.R

See deSolve simulation README for a more detailed description on how find_critical_rde_release_stat works and how we simulated 1D and 2D ODEs in deSolve.

Data

For each threshold-dependent system, we varied the release width (in 1D) or diameter (in 2D) in SLiM and recorded outputs in compressed folders of data

summary-statistics.Rmd shows how summary statistics, such as the SLiM critical release size, were calculated from SLiM data. These summary statistics are provided in the following Excel sheets:

• 1D:
  • critical-bubble-underdominance-alleles.xlsx
  • rectangle1D-underdominance-alleles.xlsx
  • rectangle1D-homing-gene-drive.xlsx
  • rectangle1D-tade-modification.xlsx
• 2D:
  • circle2D-tade-modification.xlsx
  • circle2D-tade-suppression.xlsx

Plotting

• plotting.Rmd shows how each subplot was created
• Subplots were arranged in Adobe Illustrator 2025

Contact

For any questions about the code, please email Isabel at [email protected]