Table 4 Parameter estimates (to 3 d.p.) under null and alternative hypotheses for branch-site Model A (four parameter version), for six significant branch/site combinations. Background site classes are: 0 (0 < ω0 < 1), 1 (ω1 = 1), 2a (0 < ω0 < 1) and 2b (ω1 = 1). Foreground site classes are: 0 (0 < ω0 < 1), 1 (ω1 = 1), 2a (ω2 ≥ 1) and 2b (ω2 ≥ 1). The six branches (a, b, c, d, e, f) are shown in Fig. 1
Branch | Amino Acid Position (gene) | Model | Parameter | 0 | 1 | 2a | 2b |
|---|---|---|---|---|---|---|---|
a | 109 (ND4) | Model A (Null) | Proportion | 0.913 | 0.082 | 0.004 | 0.000 |
|  |  | Background ω | 0.040 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 1.000 | 1.000 | |
| Â | Model A (Alternative) | Proportion | 0.915 | 0.082 | 0.003 | 0.000 | |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 998.999 | 998.999 | |
b | 137 (ND6) | Model A (Null) | Proportion | 0.917 | 0.083 | 0.001 | 0.000 |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 1.000 | 1.000 | |
| Â | Model A (Alternative) | Proportion | 0.917 | 0.083 | 0.001 | 0.000 | |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 352.529 | 352.529 | |
c | 10 (ND2) | Model A (Null) | Proportion | 0.908 | 0.082 | 0.010 | 0.001 |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 1.000 | 1.000 | |
| Â | Model A (Alternative) | Proportion | 0.917 | 0.082 | 0.000 | 0.000 | |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 70.079 | 70.079 | |
d | 448 (ND4) | Model A (Null) | Proportion | 0.914 | 0.083 | 0.003 | 0.000 |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 1.000 | 1.000 | |
| Â | Model A (Alternative) | Proportion | 0.917 | 0.083 | 0.000 | 0.000 | |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 682.538 | 682.538 | |
e | 171 (COXIII) | Model A (Null) | Proportion | 0.884 | 0.080 | 0.034 | 0.003 |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 1.000 | 1.000 | |
| Â | Model A (Alternative) | Proportion | 0.911 | 0.082 | 0.006 | 0.001 | |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 6.409 | 6.409 | |
f | 365 (ND5) | Model A (Null) | Proportion | 0.909 | 0.082 | 0.008 | 0.001 |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 1.000 | 1.000 | |
| Â | Model A (Alternative) | Proportion | 0.916 | 0.083 | 0.001 | 0.000 | |
|  |  | Background ω | 0.041 | 1.000 | 0.041 | 1.000 | |
|  |  | Foreground ω | 0.041 | 1.000 | 10.593 | 10.593 |