Fig 1.
Phylogeny of real rabies virus whole genome sequences from Tanzania and root-to-tip divergence.
(A) The time-scaled tree [43] used to generate the root-to-tip divergence plot and to calculate the per-generation substitution rate. The inset map shows the approximate locations that the samples were collected from, and the lineages present in each location. Map point size represents the number of sequences in this dataset from district centroid locations. Base map data is from Natural Earth (naturalearthdata.com), via the maps R package. (B) The corresponding root-to-tip divergence plot. Point colours represent RABV lineage.
Fig 2.
Temporal genetic divergence varies under two models of mutation.
(A) Root-to-tip divergence plots for synthetic sequences produced using time-based and generation-based mutation models, equivalent to 2 substitutions per genome per generation and (B) equivalent to 0.2 substitutions per genome per generation. Note that the y-axis scales differ by an order of magnitude between A and B. These data are from running mutation models over the same single transmission tree and have a case sampling rate of 5% (i.e., 621 cases sampled of 12,434 total). (C) The R2 values obtained from regression through the origin of root-to-tip divergence of synthetic data from the time-based and generation-based models. Point colour indicates the mutation model used to generate the data. Lines represent beta regressions with logit links fit to data points, and shading represents the 95% prediction interval. The X axis is log scaled. 5% of cases were sampled here; sampling rate had little effect on R2 (S3 Fig).
Fig 3.
Accuracy of per-generation substitution rate predictions for different numbers of sequences, substitution rates and sampling rates.
Facets indicate case sampling rate. The dotted line represents perfect accuracy. X axis and colour scale are log transformed.
Fig 4.
Probability distributions of the mean per-generation substitution rate and substitutions occurring over generations.
(A) estimated probability distribution of the per genome per generation substitution rate from Tanzanian RABV sequences, with underlying histogram of multiplied Bayesian posteriors of clock rate and generation interval. (B) probability distribution of SNPs occurring over 1, 5 and 10 generations. The λ value for a Poisson rate of SNP occurrence is drawn from the SNPs per generation distribution fitted in Fig 4A. Black bars represent the 95% confidence intervals (which are very tight).