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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