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
From: Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient
|
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
|
| |
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
|
| |
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
|
| |
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
|
| |
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
|
| |
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
|
| |
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
|
