The molecular clock behaviour of the HCV genome. Three separate data sets are shown: among host subtype 1a (green), among host subtype 1b (blue) and within-host (red). Separate parameters were estimated for each of 21 partitions spanning the HCV coding region (see genome schematic and partition numbering at top of Figure). The alternating white and grey bars are for visual clarity only; nucleotide numbering according to the H77 reference genome is show at the bottom. (a) Estimated mean evolutionary rates. For each partition and data set, the vertical bar represents the range of the 95% HPD credible region and the circle represents the point estimate of the mean rate. (b) Estimated coefficient of variation (COV) parameters for each partition and data set, which represent the among-lineage rate heterogeneity. The vertical bars represent the range of the HPD credible region and the circle shows the estimated COV value. (c) Estimated codon rate ratio (CRR) values, which represent the ratio of the evolution rate at codon positions 1 and 2 to that at codon position 3. As before, the vertical bar represents the range of the 95% HPD credible region and the circle represents the point estimate of CRR.
Gray et al. BMC Evolutionary Biology 2011 11:131 doi:10.1186/1471-2148-11-131