Table 2.
Summary statistics for detecting selection using branch-site and site models of PAML4.8
| Model | p | L | Estimate of parameters | df | 2ΔL | 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 %