Table 2. Likelihood values and parameter estimates for the H gene in PPRV.
| Model | npa | -ln L | Estimates of parameters | P-value | PSSb | ||
|---|---|---|---|---|---|---|---|
| M0 (one-ratio) | 72 | 7368.0629 | ω = 0.2087 | -- | |||
| M3 (discrete) | 76 | 7334.0967 | p0 = 0.4579 | p1 = 0.5303 | p2 = 0.0117 | P < 0.001 | aa246** |
| ω0 = 0.0039 | ω1 = 0.3535 | ω2 = 2.0661 | |||||
| M1 (Nearly Neutral) | 73 | 7338.8989 | p0 = 0.8883 | p1 = 0.1118 | -- | ||
| ω0 = 0.1254 | ω1 = 1.0000 | ||||||
| M2 (Positive Selection) | 75 | 7338.8989 | p0 = 0.8883 | p1 = 0.0543 | p2 = 0.0573 | NS | |
| ω0 = 0.1253 | ω1 = 1.0000 | ω2 = 1.0000 | |||||
| M7 (β) | 73 | 7336.5503 | p = 0.4194 | q = 1.5364 | -- | ||
| M8 (β & ω) | 75 | 7334.4513 | p0 = 0.9946 | p1 = 0.0053 | p = 0.5113 | P < 0.05 | aa246* |
| q = 1.9956 | ω = 2.6148 | ||||||
a. Number of parameters.
b.Positive-selection sites (PSS) are inferred at posterior probabilities > 0.95. The lists of sites are identical between Naive Empirical Bayes (NEB) and Bayes Empirical Bayes (BEB) analysis in M2 and M8, while only Naive Empirical Bayes (NEB) analysis was used in M3.
*: P>95%;
**: P>99%