Table 2 Summary statistics for detecting selection using branch-site and site models of PAML4.8

M0: one-ratio

1

−33,700

ω: 0.160

None

M1a: nearly neutral

2

−33,148

p ₀ = 0.727, p ₁ = 0.273 ω ₀ = 0.125, ω ₁ = 1.00

Not allowed

M2a: positive selection

4

−33,148

p ₀ = 0.727, p ₁ = 0.182, p ₂ = 0.090; ω ₀ = 0.125, ω ₁ = 1.000, ω ₂ = 1.000

2

0

M3: discrete

5

−32,727

p ₀ = 0.212, p ₁ = 0.594, p ₂ = 0.194; ω ₀ = 0.038, ω ₁ = 0.180, ω ₂ = 1.934

4

1946.50^***

21,24,25,27,28 ~ 43,44,45,46,47,48,49,51 ~ 57,60,103,105,106,134,136,137,138,243,279,325,361,362,373,492,493,494,548,549,550 ~ 554,556,557,558,560,561,562,563,566,567

M7: β

2

−32,705

p = 0.642, q = 1.628

Not allowed

M8: β & ω

4

−32,583

p ₀ = 0.858, p = 0.971, q = 4.418, p ₁ = 0.142, ω = 4.858

2

244.99^***

21,24,25,29,32,35,37,39,40,42,46,49,53,54,56,57,103,134,362,493,550,551,563.

model A (C19-GA2ox)

4

−33,132

p ₀ = 0.509, p ₁ = 0.189, p ₂ = 0.302, ω ₂ = 8.762

1

6.26^*

393,520

model A (C20-GA2ox)

4

−33,129

p ₀ = 0.446, p ₁ = 0.167, p ₂ = 0.386, ω ₂ = 47.691

1

15.83^***

150,184,217,232,239,287,289,294,299,383,519,531,535

model A (GA20ox)

4

−33,110

p ₀ = 0.442, p ₁ = 0.163, p ₂ = 0.395, ω ₂ = 999.000

1

39.77^***

65,71,81,114,148,149,159,161,172,190,214,264,291,304,330,348,377,381,384,385,417,437,447,471,477,507,515,519,524

model A (GA3ox)

4

−33,132

p ₀ = 0.466, p ₁ = 0.175, p ₂ = 0.358, ω ₂ = 7.881

1

9.51^**

156,158,163,232,288,339,505,525

model A (GAox-A)

4

−33,135

p ₀ = 0.556, p ₁ = 0.205, p ₂ = 0.238, ω ₂ = 13.489

1

10.41^**

340

model A (GAox-B)

4

−33,133

p ₀ = 0.464, p ₁ = 0.174, p ₂ = 0.363, ω ₂ = 39.904

1

14.41^***

197,231,343,352,353,354,416,444,469,471,525,530

model A (GAox-C)

4

−33,136

p ₀ = 0.465, p ₁ = 0.174, p ₂ = 0.362, ω ₂ = 5.019

1

3.97^*

342,439

model A (GAox-D)

4

−33,124

p ₀ = 0.424, p ₁ = 0.160, p ₂ = 0.417, ω ₂ = 21.542

1

17.55^***

84,160,161,213,231,233,259,263,299,304,310,335,339,341,347,352,364,366,423,427,453,457,470,475,485,511,517,525,545