Fig. 1: Per-site πN and πS values simulated under a model of primarily weakly deleterious mutations (top row), and a model of primarily strongly deleterious mutations (bottom row), occurring in the SARS-CoV-2 genome.
The leftmost column provides the deleterious distribution of fitness effects (DFE) from which non-synonymous mutations were sampled under these two respective models; the middle column presents \({\pi }_{N}\) (red) and \({\pi }_{S}\) (blue) values for 10 kb non-overlapping windows of the genome, as well as the genome-wide values (30 kb); the rightmost column presents \({\pi }_{N}\) – \({\pi }_{S}\) values across the same genomic windows, and genome-wide. Point estimates represent mean values across 200 simulation replicates, with the standard deviation plotted as 68% confidence intervals. Simulations were performed using SLiM4.126. Every third site of the genome was simulated as being strictly neutral (i.e., synonymous for the purpose of analysis), while all other sites were drawn from the respective DFE (i.e., non-synonymous for the purpose of analysis). Following the baseline model recommendations of refs. 15,16, the following parameterizations were utilized: infection bottleneck size = 1; recombination rate = 5.5e-5 events/site/cycle; mutation rate/site/replication = 2.135e-6; carrying capacity = 1e5. Simulations were run for 168 N generations (corresponding to an infection of 7 days), with 100 genomes sampled at the end-point. As per ref. 1, SNPs with an allele frequency less than 2.5% were masked when estimating \(\pi\). Source data are provided as a Source Data file. All code for replicating these results is available on GitHub (https://github.com/vivaksoni/Gu_etal_2023_response).
