Figure legends

Figure 1: Effective reproductive number (R e) as a function of time (years). Each considered epoch was approximately five years. Shaded area indicates the 95% highest probability density. First row are parameter estimates under the Bayesian Sampled Ancestor Birth-Death Skyline model, second raw under the Bayesian Birth-Death Skyline model. On the left-hand side, with common δ and sampling proportion parameter across all epochs, while on the right-hand side with a variable sampling proportion parameter.
Figure 2: Violin plots of sampling proportion parameter (s) estimates for different time intervals (x-axis) under the Bayesian Sampled Ancestor Birth-Death Skyline (left) and the Bayesian Birth-Death Skyline (right) models. Dots indicate the medians.
Figure 3: Bayesian Skyline Plot of virus demographic changes (y-axis in log scale) over time. Shaded area indicates the 95% highest probability density.