Table 3.
Parameter estimates and likelihood values for branch-site models among sites and lineages of PEBP
| Branch-site model | Foreground branch | Estimate of parameters | Model comparison | 2*|lnL1 − lnL2| | df | pLRT | Selected sites |
|---|---|---|---|---|---|---|---|
| Model A | FT | proportion P = 0.54412, 0.44507, 0.00595, 0.00486 |
Model A vs Model Aa |
3.816 | 1 | 0.05 | 19,106 |
| background ω = 0.13622, 1.00000, 0.13622, 1.00000 | |||||||
| foreground ω1 = 0.13622, 1.00000, 26.81509, 26.81509 | |||||||
| TFL1 | proportion P = 0.16400, 0.49980, 0.08306, 0.25314 |
Model A vs Model Aa |
10.381 | 1 | 0.0013** | 11,18 | |
| background ω = 0.14566, 1.00000, 0.14566, 1.00000 | |||||||
| foreground ω = 0.14566, 1.00000, 999.00000, 999.00000 | |||||||
| CEN | proportion P = 0.23775, 0.76225, 0.00000, 0.00000 |
Model A vs Model Aa |
2E-06 | 1 | P > 0.05 | – | |
| background ω = 0.14634, 1.00000, 0.14634, 1.00000 | |||||||
| foreground ω = 0.14634, 1.00000, 1.00000, 1.00000 | |||||||
| BFT | proportion P = 0.20425, 0.66599, 0.03046, 0.09930 |
Model A vs Model Aa |
2.878 | 1 | P > 0.05 | – | |
| background ω = 0.12885, 1.00000, 0.12885, 1.00000 | |||||||
| foreground ω = 0.12885, 1.00000, 7.38132, 7.38132 | |||||||
| (FT, TFL1, CEN, BFT) | proportion P = 0.23291, 0.72041, 0.01140, 0.03528 |
Model A vs Model Aa |
0.521 | 1 | P > 0.05 | – | |
| background ω = 0.15263, 1.00000, 0.15263, 1.00000 | |||||||
| foreground ω = 0.15263, 1.00000, 10.76576, 10.76576 |
Significant chi-squared comparisons are indicated with * (pLRT < 0.05), ** (pLRT < 0.01), and *** (pLRT < 0.001). Positively selected sites in the foreground lineages were detected by Bayes Empirical Bayes analysis with a probability ≥ 0.7