Table 3 Parameter estimates under different site models and statistics of the likelihood ratio (2Δl) hypothesis tests in PAML

M0: one ratio

ω = 0.25443

28843.35

M0/M3

4

1666.50

1.11 x 10⁻³⁵⁹

M3: discrete

ω₀ = 0.03317;

ω₁ = 0.22423;

ω₂ = 0.62748;

p₀ = 0.26344;

p₁ = 0.47946;

p₂ = 0.2571

28010.09

M1a: neutral

ω₀ = 0.18188;

ω₁ = 1.00000;

p₀ = 0.73346;

p₁ = 0.26654

28338.75

M1/M2

2

14.56

6.87 x 10⁻⁰⁴

M2a: selection

ω₀ = 0.184690;

ω₁ = 1.000000;

ω₂ = 1.879270;

p₀ = 0.72964;

p₁ = 0.25444;

p₂ = 0.01592

28331.46

M7: beta

p = 0.70821;

q = 1.65979

27977.46

M7/M8

2

35.54

1.92 x 10⁻⁰⁸

M8: beta & w

p₀ = 0.96464;

p = 0.85258;

q = 2.56188;

p₁ = 0.03536;

ω = 1.262270

27959.69

18K (67.8 %);

38K (53.0 %),

58I (99.9 %);

151K (52.3 %)

204L (98.2 %);

208A (92.3 %);

236S (95.5 %)

Model A (null)

p₀ = 0.52400;

p₁ = 0.18218;

p_2a = 0.21802;

p_2b = 0.07580;

ω₀ = 0.16817;

ω₁ = 1.00000;

background: ω_2a = 0.16817;

ω_2b = 1.00000;

foreground: ω_2a = 1.00000;

ω_2b = 1.00000

28279.91

Null/

Alt.

1

13.89

1.94 x 10⁻⁰⁴

21P (95.7 %);

22T (100.0 %);

40S (99.0 %);

53F (98.7 %);

84G (97.2 %);

144G (99.8 %);

179T (98.5 %);

201F (98.2 %)

205G (99.8 %);

214I (95.3 %);

231S (100.0 %);

239R (95.9 %);

240K (97.2 %);

243E (100.0 %);

253Y (99.6 %);

265G (99.8 %)

Model A

(alternative)

p₀ = 0.58498;

p₁ = 0.20363;

p_2a = 0.15681;

p_2b = 0.05458;

ω₀ = 0.17009;

ω₁ = 1.00000;

background:

ω_2a = 0.17009;

ω_2b = 1.00000;

foreground:

ω_2a = 1.97553;

ω_2b = 1.97553

28272.97