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. 2015 Sep 29;15:207. doi: 10.1186/s12862-015-0490-2

Table 2.

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

Model p L Estimate of parameters df L Positively Selected Sitesa
Site-specific models
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.
Branch-site model
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

p is the number of free parameters in the ω distribution

*significant at p value < 0.05 level, **significant at p value < 0.01 level, ***significant at p value < 0.001 level

apositively selected sites identified under site and branch-site tests with PP ≥ 95 %