TABLE 1.
Molecular clock and TMRCA estimations of both genome segments of vvIBDV based on various approaches
| Genome segment | Length (bp) | No. of taxa | lnLa
|
LRT (P) (clock rejection)b | Yr of TMRCA (range)c
|
|||
|---|---|---|---|---|---|---|---|---|
| M0 | M1 | LR | ML | BMCMC | ||||
| vvfVP2 | 1,323 | 24 | −2,813.171 | −2,828.190 | 0.118 (no) | 1960 (1942-1969) | 1966 (1955-1977) | 1965 (1952-1975) |
| vvpVP2 | 330 | 153 | −3,257.785 | −3,361.408 | 0.003 (yes) | 1968 (1943-1977) | 1946 (1924-1968) | 1962 (1950-1973) |
| vvVP1 | 2,322 | 9 | −4,291.567 | −4,299.338 | 0.03 (yes) | 1981 (NA-1989) | 1979 (1972-1986) | 1974 (1953-1985) |
| Site-stripped vvVP1 | 2,307 | 9 | −4,115.234 | −4,120.421 | 0.168 (no) | 1984 (1972-1988) | 1981 (1976-1986) | 1980 (1973-1988) |
a
lnL represents the natural log likelihood of the global-clock (M1) and no-clock (M0) models calculated in PAML under the Hasegawa-Kishino-Yano nucleotide substitution model.
b
The molecular clock is rejected when P is <0.05 under the LRT.
c
The BMCMC TMRCA refers to the TMRCAs estimated with BEAST under the assumption of a molecular clock. TMRCAs estimated based on the corresponding approaches are presented as the best fit (for LR and ML) or mean (for BMCMC) value, with the 95% CI (for LR and ML) or high-probability density (for BMCMC) in parentheses. NA, not applicable.