Table 1. Bayesian estimates of substitution rates (×10−3 nucleotide substitutions per site per year) and TMRCAs (in year) inferred from partial N and F genes. Best-fitting clock models and the corresponding parameter estimates are in bold.
| Gene | Group | n | Nucleotide substitution model | Clock model | Marginal log likelihood | 2ln(BF) | Mean rate in ×10−3 subs/site/yr (95% HPD) | TMRCA in year (95% HPD) | Relaxed clock coefficient of variation (95% HPD) |
|---|---|---|---|---|---|---|---|---|---|
| Nucleocapsid | All | 131 | GTR | Strict | −2027.339 | 1.05 (0.80–1.31) | 1887 (1852–1887) | NA | |
| Relax | −1989.106 | 76.466 | 1.22 (0.83–1.65) | 1898 (1818–1944) | 1.08 (0.60–1.70) | ||||
| GTR+G | Strict | −2006.608 | 1.12 (0.83–1.43) | 1880 (1838–1912) | NA | ||||
| Relax | −1965.744 | 81.728 | 1.31 (0.86–1.84) | 1893 (1798–1947) | 1.15 (0.65–1.79) | ||||
| GTR+I+G | Strict | −2006.666 | 1.11 (0.82–1.44) | 1878 (1836–1911) | NA | ||||
| Relax | −1965.227 | 82.878 | 1.34 (0.88–1.88) | 1895 (1808–1946) | 1.16 (0.67–1.82) | ||||
| Lineage IV | 100 | GTR | Strict | −1182.504 | 1.80 (1.31–2.33) | 1988 (1984–1992) | NA | ||
| Relax | −1166.582 | 31.844 | 1.90 (1.36–2.50) | 1988 (1981–1992) | 0.99 (0.32–1.78) | ||||
| GTR+G | Strict | −1180.553 | 1.88 (1.33–2.52) | 1989 (1984–1992) | NA | ||||
| Relax | −1164.267 | 32.572 | 1.96 (1.37–2.63) | 1988 (1981–1992) | 1.05 (0.35–1.81) | ||||
| GTR+I+G | Strict | −1181.018 | 1.89 (1.35–2.53) | 1988 (1984–1992) | NA | ||||
| Relax | −1165.791 | 30.454 | 1.95 (1.34–2.62) | 1987 (1981–1992) | 0.99 (0.32–1.83) | ||||
| Fusion protein | All | 116 | GTR | Strict | −1861.382 | 1.922 | 0.68 (0.51–0.87) | 1912 (1883–1938) | NA |
| Relax | −1862.343 | 0.69 (0.50–0.86) | 1911 (1876–1939) | 0.14 (0.0006–0.43) | |||||
| GTR+G | Strict | −1858.701 | 0.70 (0.50–0.91) | 1911 (1879–1937) | NA | ||||
| Relax | −1855.779 | 5.844 | 0.69 (0.50–0.91) | 1910 (1873–1939) | 0.16 (0.0017–0.47) | ||||
| GTR+I+G | Strict | −1859.83 | 0.69 (0.51–0.89) | 1911 (1879–1934) | NA | ||||
| Relax | −1856.994 | 5.672 | 0.69 (0.50–0.90) | 1910 (1873–1939) | 0.16 (0.0018–0.48) | ||||
| Lineage IV | 103 | GTR | Strict | −1410.938 | 0.78 (0.50–1.1) | 1987 (1970–1992) | NA | ||
| Relax | −1403.387 | 15.102 | 0.78 (0.49–1.1) | 1987 (1976–1992) | 0.55 (0.00005–1.0) | ||||
| GTR+G | Strict | −1416.085 | 0.78 (0.49–1.1) | 1986 (1968–1992) | NA | ||||
| Relax | −1406.868 | 18.434 | 0.78 (0.49–1.1) | 1987 (1977–1992) | 0.55 (0.0002–0.99) | ||||
| GTR+I+G | Strict | −1414.696 | 0.79 (0.50–1.12) | 1986 (1971–1992) | NA | ||||
| Relax | −1408.031 | 13.33 | 0.81 (0.52–1.16) | 1987 (1979–1992) | 0.56 (0.001–1.01) |
n: Number of sequences; BF: Bayes Factor; TMRCA: Time to the most recent common ancestor; HPD: Highest Posterior Density; CoV: Coefficient of Variation. Cases in which the coefficient of variation (CoV) does not encompass zero are in italic.