Table 3.
Estimated nucleotide substitution rates for the S and N genes.
| Dataset | Data Best Fit Molecular Clock * | Data Best Fit Tree Prior | Geometric Mean Rate (×10−4) ** | 95% HPD Interval (×10−4) *** |
|---|---|---|---|---|
| D1: Complete S gene | RLC | Constant | 5.23 | 3.81–6.53 |
| D2: S gene without recombinant regions | RLC | Exponential | 7.98 | 6.18–10.02 |
| D3: Complete N gene | RLC | Constant | 6.58 | 4.34–9.03 |
| D4: N gene without recombinant regions | RLC | BSP | 3.24 | 2.12–4.52 |
* Random local clock model (RLC). ** The geometric mean nucleotide substitution rate (substitutions/site/year) was inferred from the data that best fit the molecular clock and coalescent tree prior of constant population size, exponential population size, and Bayesian skyline plot (BSP). *** Highest posterior density (HPD).