TABLE 2.
Orthocoronavirus ages by different models in this study using amino acid sequences. Calibration confidence intervals at 2.5–97.5% are 14–20 MY for Bat-17 MYA, 30–42 MY for Bat-35 MYA and 134–167 MY for Bird-150 MYA. Mean and 95% highest posterior density (HPD) only are shown for the substitution rate (per site per million years).
| Orthocoronaviruses | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Hosts | Bat | Bat & Bird | Bat & Bird | Bat | Bat & Bird | Bat & Bird | Bat & Bird | Bat | Bat & Bird | Bat & Bird | Bat | Bat & Bird | Bat & Bird | Bat & Bird |
| Model | ||||||||||||||
| Clock | Relaxeda | Relaxed | Relaxed | Relaxeda | Relaxeda | Relaxeda | Relaxed | Strict | Strict | Strict | Strict | Strict | Strict | Strict |
| Site model | LG | LG | LG | LG | LG | LG | LG | LG | LG | LG | LG | LG | LG | LG |
| Calibration | Bat-17 MYA | Bat-17 MYA | Bat-17 MYA + Bird-150 MYA | Bat-35 MYA | Bat-35 MYA | Bat-35 MYA + Bird-150 MYA | Bird-150 MYA | Bat-17 MYA | Bat-17 MYA | Bat-17 MYA + Bird-150 MYA | Bat-35 MYA | Bat-35 MYA | Bat-35 MYA + Bird-150 MYA | Bird-150 MYA |
| Age | ||||||||||||||
| Mean | 178.5 | 239.2 | 176.9 | 347.6 | 492 | 234.7 | 168 | 213.7 | 264.9 | 167.8 | 417.8 | 531.7 | 185.9 | 163.4 |
| Median | 160.4 | 223.4 | 170 | 305.8 | 465.2 | 218.4 | 162.8 | 198 | 246 | 166.4 | 391.3 | 493.2 | 184.4 | 162 |
| 95% HPD | 21.2–375.9 | 85.6–423.9 | 136–231 | 38.2–748.1 | 221.5–832.4 | 141.5–361.7 | 134.4–210 | 90.7–363.4 | 123.8–446.7 | 143.1–197.2 | 190.9–708 | 240.7–899.1 | 153.9–219.8 | 139–191.5 |
| Range | 14.9–1565.5 | 34.4–1077.3 | 126–765 | 31.2–3176.9 | 92.2–1504.1 | 136.2–792.2 | 129.1–454.8 | 68.5–942.8 | 72.2–760.4 | 121.5–240.3 | 106.8–1265.2 | 195.5–2897.1 | 139.1–262.8 | 124.8–240 |
| Bat Clade Age | ||||||||||||||
| Mean | 178.5 | 171.3 | 139.7 | 347.6 | 358.9 | 171.1 | 131 | 213.7 | 199.8 | 139.7 | 417.8 | 399.3 | 160 | 134.7 |
| Median | 160.4 | 160.3 | 137 | 305.8 | 340.6 | 165.5 | 129.4 | 198 | 186.4 | 138.4 | 391.3 | 367.2 | 158.9 | 133.2 |
| 95% HPD | 21.2–375.9 | 61.9–306.1 | 97–187 | 38.2–748.1 | 164.5–603.1 | 93.4–259.8 | 89.8–173.4 | 90.7–363.4 | 92.3–338.1 | 108.1–172.6 | 190.9–708 | 185.5–687.6 | 123.9–198 | 105.5–167.8 |
| Range | 14.9–1565.5 | 23.4–711.8 | 68–352 | 31.2–3176.9 | 63.6–1127.4 | 54.6–560.5 | 67.6–350.4 | 68.5–942.8 | 85.8–829.2 | 88.5–215.2 | 106.8–1265.2 | 134.9–2095 | 101.2–236.5 | 88.1–218.5 |
| Substitution rate | ||||||||||||||
| Mean | 2.41E-3 | 1.81E-3 | 2.20E-3 | 1.18E-3 | 9.02E-4 | 1.81E-3 | 2.36E-3 | 1.52E-3 | 1.63E-3 | 2.20E-3 | 7.71E-4 | 8.13E-4 | 1.91E-3 | 2.30E-3 |
| 95% HPD | 5.84E-4 –5.49E-3 | 8.29E-4 –2.94E-3 | 1.65E-3 –2.75E-3 | 2.50E-4 –2.79E-3 | 3.71E-4 –1.46E-3 | 1.04E-3 –2.69E-3 | 1.67E-3 -2.99E-3 | 6.79E-4 -2.51E-3 | 7.17E-4 -2.62E-3 | 1.79E-3 -2.60E-3 | 3.41E-4 -1.27E-3 | 3.63E-4 -1.32E-3 | 1.55E-3 -2.27E-3 | 1.86E-3 -2.75E-3 |
a
Low ESS (<200) for some parameters, see text.