The violin plots of the posterior evolutionary rate estimated using the uniform (0, 0.01) rate prior in the nine genomic regions and over the entire ORF of the subtype 1a (A panel) and 1b (B panel) datasets.

Abstract

<p>Combined with the GTR+I+Γ substitution model and Bayesian skyline coalesent model, the MCMC procedures were run under three clock models, exoponetial, lognormal, and strict, respectively, using BEAST. The vertical axis measures the substitution rate multiplied by 10⁻³ (substitution/site/year). The horizontal axis indicates the nine genomic regions and the entire ORF. The left three panels show the results for the 1a dataset. The right three panels show the results for the 1b dataset. In each panel, two violins are separated in a small case on the right, which indicate the rates estimated for the routinely amplified partial Core-E1 (P-C/E1) and partial NS5B (P-NS5B) regions.</p