Comparisons to SARS-CoV-2 phylogeny.
Phylogenies downsampled at 10% from the full (18,514 tips) SARS-CoV-2 genome phylogeny (following the subsampling strategy described above) were used to calculate the phylogenetic η for each subtree (above the root) for each downsampled phylogeny. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. Positive time-dependent phylogenies were simulated using a time-dependent process (b(t)=0.01eαt) for α = 0.001, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 1, with branch lengths restricted to the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53).