TABLE 7.
Results of the branch-site model analysis for PHYE
| Model | Estimated parameters | λ | P-value | ||
|---|---|---|---|---|---|
| Nearly neutral | ω0 = 0.000 | p0 = 0.70 | −4822.38 | ||
| ω1 = 1.000 | p1 = 0.30 | ||||
| Branch-site | ω0−b = 0.000 | ω0−f = 0.000 | p0 = 0.76 | −4818.01 | P1 < 0.05 |
| ω1−b = 1.000 | ω1−f = 1.000 | p1 = 0.19 | P2 = 0.11 | ||
| ω0−b = 0.000 | ω2 = 32.17 | p2A = 0.04 | |||
| ω1−b = 1.000 | ω2 = 32.17 | p2B = 0.01 | |||
| Null with ω2 = 1 | ω0−b = 0.000 | ω0−f = 0.000 | p0 = 0.70 | −4819.28 | |
| ω1−b = 1.000 | ω1−f = 1.000 | p1 = 0.30 | |||
| ω0−b = 0.000 | ω2 = 1.000 | p2A = 0.00 | |||
| ω1−b = 1.000 | ω2 = 1.000 | p2B = 0.00 | |||
ω0−b/ω1−b and ω0−f/ω1−f indicate two ratios of nonsynonymous to synonymous substitutions (ω0, ω1) in the background (the interspecific and intraregional branches) and in the foreground (the interregional branches), respectively. ω2 indicates the ratio of nonsynonymous to synonymous substitutions on positively selected sites in the foreground. p0, p1, p2A, and p2B indicate the frequency of sites that have a pair of ω's in the background and foreground. The P-values above and below indicate the significance of the branch-site model tested against the nearly neutral model (test 1) and the null model with ω2 = 1 (test 2), respectively.