CAIN and ClvR modification drive parameters in SLiM

We set each 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 fixation rates and average time to fixation) using Cornell University’s Computational Biology Department’s high-performance super-computing cluster. The following sections describe constants that must be set in the SLiM model (seedbank.slim) to simulate each modification 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.

CAIN

SLiM constants

• L: 10
• b: 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: 1.0
• q: 0.1
• K: 10000
• TRACK_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: F
• FEMALE_FERTILITY_SUPPRESSION_DRIVE: F
• CAIN: T
• s_g: 0.0
• s_s: 0.0
• GERMLINE_CLEAVAGE_RATE_FEMALE: 0.941
• GERMLINE_CLEAVAGE_RATE_MALE: 0.984
• CAIN_PENETRANCE_RATE: 0.96
• INTRODUCTION_FREQUENCY: 0.1
• HETEROZYGOUS_DROP: T
• PRESEED_R1_ALLELES: F

Example command line simulation

slim -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=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 CAIN at b=0.5 and m = 1.0, with all other parameters set to their defaults. On a MacBook Pro (Apple M2 Pro CPU, 8GB RAM), this takes approximately 2 minutes to run. Note: if the SLiM file is not in your current directory, replace seedbank.slim with the path to the file.

ClvR

SLiM constants

• L: 10
• b: 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: 1.0
• q: 0.1
• K: 10000
• TRACK_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: F
• FEMALE_FERTILITY_SUPPRESSION_DRIVE: F
• CAIN: F
• s_g: 0.0
• s_s: 0.0
• GERMLINE_CLEAVAGE_RATE_FEMALE: 0.974
• GERMLINE_CLEAVAGE_RATE_MALE: 0.974
• CLVR_PENETRANCE_RATE: 1.0
• MATERNAL_CARRYOVER_RESCUE_RATE: 0.207
• INTRODUCTION_FREQUENCY: 0.1
• HETEROZYGOUS_DROP: T
• PRESEED_R1_ALLELES: F

Example command line simulation

slim -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=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 ClvR at b=0.5 and m = 1.0, with all other parameters set to their defaults. On a MacBook Pro (Apple M2 Pro CPU, 8GB RAM), this takes around 2 minutes to run. Note: if the SLiM file is not in your current directory, replace seedbank.slim with the path to the file.