Table 1.
Alignments and results of substitution rate analyses of picornaviruses
| Gene | Viral speciesa | No. of taxa | No. of ntb | Date range | Substitution model | Clock model | TMRCA (ybp)c | Substitution rate (×10−3)c | dN/dS |
|---|---|---|---|---|---|---|---|---|---|
| VP1 | Human enterovirus B (CVB2) | 51 | 231 | 1946–2008 | GTR+I+Γ | Relaxed | 72 (60–100) | 5.27 (3.57–7.06) | 0.04 |
| Human enterovirus B (CVB4) | 110 | 300 | 1959–2007 | TrN+I+Γ | Relaxed | 75 (60–95) | 5.73 (4.18–7.29) | 0.03 | |
| Encephalomyocarditis virus | 27 | 210 | 1986–2008 | K80+I | Strict | 247 (98–824) | 1.61 (0.56–2.78) | 0.03 | |
| Porcine teschovirus | 46 | 702 | 1957–2007 | GTR+I+Γ | Strict | 507 (205–832) | 1.62 (0.63–2.75) | 0.10 | |
| 3Dpol | Human enterovirus A (EV71) | 153 | 999 | 1986–2010 | TN93+I+Γ | Relaxed | 120 (97–139) | 5.53 (4.29–6.67) | 0.05 |
| Human enterovirus C (PV1) | 51 | 534 | 1982–2006 | GTR+I+Γ | Relaxed | 45 (31–69) | 11.68 (8.12–14.53) | 0.03 | |
| Foot-and-mouth disease virus (FMDV-A) | 24 | 642 | 1971–2009 | GTR+I+Γ | Strict | 152 (33–424) | 1.45 (0.70–2.24) | 0.05 | |
| Hepatitis A virus | 25 | 402 | 1976–2008 | TN93+I+Γ | Strict | 746 (429–995) | 0.89 (0.46–1.31) | 0.03 | |
| Human parechovirus | 142 | 657 | 1975–2009 | GTR+I+Γ | Relaxed | 124 (88–212) | 2.96 (1.88–3.92) | 0.04 |
a
Abbreviations are given for enterovirus and aphthovirus serotypes.
b
nt, nucleotides.
c
Mean substitution rates are shown with lower and upper 95% credibility interval bounds in parentheses.