We considered 3 suppression drives. For ClvR, we modeled ClvR male suppression, in which males with 2 ClvR drive alleles are sterile, and ClvR female suppression, in which females with 2 ClvR drive alleles are sterile. For CAIN, we only modeled CAIN male suppression, in which males with 2 CAIN drive alleles are sterile.
We set each suppression drive to their experimental parameters and varied the baseline germination rate (b) and age-dependence germination parameter (m), keeping all other seedbank parameters at their defaults. We ran 10 simulation replicates per parameter combination and obtained summary statistics (such as population elimination rates and average time to elimination) using Cornell University’s Computational Biology Department’s high-performance super-computing cluster. We also created trajectory plots for the drive frequency, effective gamete counts, and genetic load across 4 values of b.
The following sections describe constants that must be set in the
SLiM model (seedbank.slim) to simulate each suppression
drive. All other constants should not be changed from their current
values in the script. For each drive, we also include an example
simulation that can be run at the command line.
L: 10b: for heatmaps, we varied this constant from 0.05 to
1.0 in steps of 0.05. For drive trajectory plots, we explored b = 0.05,
b = 0.2, b = 0.5, and b = 1.0.m: for heatmaps, we varied this constant from 0.0 to
2.0 in steps of 0.1. For drive trajectory plots, we set m = 0.d: 1.0q: 0.1K: 10000TRACK_FREQUENCIES: T if creating trajectory plots for
these parameters. F if not.BASELINE_OVULE_AVG: 60 for default fecundity. 20 for
lower fecundity.BASELINE_EFFECTIVE_POLLEN_AVG: 180 for default
fecundity. 60 for lower fecundity.MALE_FERTILITY_SUPPRESSION_DRIVE: TFEMALE_FERTILITY_SUPPRESSION_DRIVE: FCAIN: Fs_g: 0.0s_s: 0.0GERMLINE_CLEAVAGE_RATE_FEMALE: 0.974GERMLINE_CLEAVAGE_RATE_MALE: 0.974CLVR_PENETRANCE_RATE: 1.0MATERNAL_CARRYOVER_RESCUE_RATE: 0.207INTRODUCTION_FREQUENCY: 0.1HETEROZYGOUS_DROP: TPRESEED_R1_ALLELES: Fslim -d L=10 -d b=0.5 -d m=1.0 -d d=1.0 -d q=0.1 -d K=10000 -d TRACK_FREQUENCIES=F -d BASELINE_OVULE_AVG=60 -d BASELINE_EFFECTIVE_POLLEN_AVG=180 -d MALE_FERTILITY_SUPPRESSION_DRIVE=T -d FEMALE_FERTILITY_SUPPRESSION_DRIVE=F -d CAIN=F -d s_g=0.0 -d s_s=0.0 -d GERMLINE_CLEAVAGE_RATE_FEMALE=0.974 -d GERMLINE_CLEAVAGE_RATE_MALE=0.974 -d CLVR_PENETRANCE_RATE=1.0 -d MATERNAL_CARRYOVER_RESCUE_RATE=0.207 -d INTRODUCTION_FREQUENCY=0.1 -d HETEROZYGOUS_DROP=T -d PRESEED_R1_ALLELES=F seedbank.slim
This simulates the ClvR male suppression drive with b=0.5 and m = 1.0
and all other parameters set to their defaults. On a MacBook Pro (Apple
M2 Pro CPU, 8GB RAM), this takes slightly less than 2 minutes to run.
Note: if the SLiM file is not in your current directory, replace
seedbank.slim with the path to the file.
L: 10b: for heatmaps, we varied this constant from 0.05 to
1.0 in steps of 0.05. For drive trajectory plots, we explored b = 0.05,
b = 0.2, b = 0.5, and b = 1.0.m: for heatmaps, we varied this constant from 0.0 to
2.0 in steps of 0.1. For drive trajectory plots, we set m = 0.d: 1.0q: 0.1K: 10000TRACK_FREQUENCIES: T if creating trajectory plots for
these parameters. F if not.BASELINE_OVULE_AVG: 60 for default fecundity. 20 for
lower fecundity.BASELINE_EFFECTIVE_POLLEN_AVG: 180 for default
fecundity. 60 for lower fecundity.MALE_FERTILITY_SUPPRESSION_DRIVE: FFEMALE_FERTILITY_SUPPRESSION_DRIVE: TCAIN: Fs_g: 0.0s_s: 0.0GERMLINE_CLEAVAGE_RATE_FEMALE: 0.974GERMLINE_CLEAVAGE_RATE_MALE: 0.974CLVR_PENETRANCE_RATE: 1.0MATERNAL_CARRYOVER_RESCUE_RATE: 0.207INTRODUCTION_FREQUENCY: 0.1HETEROZYGOUS_DROP: TPRESEED_R1_ALLELES: Fslim -d L=10 -d b=0.5 -d m=1.0 -d d=1.0 -d q=0.1 -d K=10000 -d TRACK_FREQUENCIES=F -d BASELINE_OVULE_AVG=60 -d BASELINE_EFFECTIVE_POLLEN_AVG=180 -d MALE_FERTILITY_SUPPRESSION_DRIVE=F -d FEMALE_FERTILITY_SUPPRESSION_DRIVE=T -d CAIN=F -d s_g=0.0 -d s_s=0.0 -d GERMLINE_CLEAVAGE_RATE_FEMALE=0.974 -d GERMLINE_CLEAVAGE_RATE_MALE=0.974 -d CLVR_PENETRANCE_RATE=1.0 -d MATERNAL_CARRYOVER_RESCUE_RATE=0.207 -d INTRODUCTION_FREQUENCY=0.1 -d HETEROZYGOUS_DROP=T -d PRESEED_R1_ALLELES=F seedbank.slim
This simulates the ClvR female suppression drive with b=0.5 and m =
1.0 and all other parameters set to their defaults. On a MacBook Pro
(Apple M2 Pro CPU, 8GB RAM), this takes around 3 minutes to run. Note:
if the SLiM file is not in your current directory, replace
seedbank.slim with the path to the file.
L: 10b: for heatmaps, we varied this constant from 0.05 to
1.0 in steps of 0.05. For drive trajectory plots, we explored b = 0.05,
b = 0.2, b = 0.5, and b = 1.0.m: for heatmaps, we varied this constant from 0.0 to
2.0 in steps of 0.1. For drive trajectory plots, we set m = 0.d: 1.0q: 0.1K: 10000TRACK_FREQUENCIES: T if creating trajectory plots for
these parameters. F if not.BASELINE_OVULE_AVG: 60 for default fecundity. 20 for
lower fecundity.BASELINE_EFFECTIVE_POLLEN_AVG: 180 for default
fecundity. 60 for lower fecundity.MALE_FERTILITY_SUPPRESSION_DRIVE: TFEMALE_FERTILITY_SUPPRESSION_DRIVE: FCAIN: Ts_g: 0.0s_s: 0.0GERMLINE_CLEAVAGE_RATE_FEMALE: 0.941GERMLINE_CLEAVAGE_RATE_MALE: 0.984CAIN_PENETRANCE_RATE: 0.96INTRODUCTION_FREQUENCY: 0.1HETEROZYGOUS_DROP: TPRESEED_R1_ALLELES: Fslim -d L=10 -d b=0.5 -d m=1.0 -d d=1.0 -d q=0.1 -d K=10000 -d TRACK_FREQUENCIES=F -d BASELINE_OVULE_AVG=60 -d BASELINE_EFFECTIVE_POLLEN_AVG=180 -d MALE_FERTILITY_SUPPRESSION_DRIVE=T -d FEMALE_FERTILITY_SUPPRESSION_DRIVE=F -d CAIN=T -d s_g=0.0 -d s_s=0.0 -d GERMLINE_CLEAVAGE_RATE_FEMALE=0.941 -d GERMLINE_CLEAVAGE_RATE_MALE=0.984 -d CAIN_PENETRANCE_RATE=0.96 -d INTRODUCTION_FREQUENCY=0.1 -d HETEROZYGOUS_DROP=T -d PRESEED_R1_ALLELES=F seedbank.slim
This simulates the CAIN male suppression drive with b=0.5 and m = 1.0
and all other parameters set to their defaults. On a MacBook Pro (Apple
M2 Pro CPU, 8GB RAM), this takes around 3 minutes to run. Note: if the
SLiM file is not in your current directory, replace
seedbank.slim with the path to the file.