Table 2. Site model tests on subset of fish or mammalian C3 genes.
| Model | np | lnL | parameter | Model comparison | 2Δ(lnL) | P-value | positive selected sites1 |
| Data set: mammals | |||||||
| M0 (one ratio) | 27 | −41738.40 | ω = 0.178 | None | |||
| M1a (nearly neutral) | 28 | −41035.20 | p 0 = 0.794, (p 1 = 0.206) | ||||
| M2a (positive selection) | 30 | −41035.20 | p 0 = 0.794, p 1 = 0.000, (p 2 = 0.206), ω 2 = 1.00 | M2a and M1a | 0.0 | 1.0 | Not allowed2 |
| M3 (discrete) | 31 | −40858.91 | p 0 = 0.266, p 1 = 0.530, (p 2 = 0.204), ω 0 = 0.027, ω 1 = 0.132, ω 2 = 0.706 | M3 and M0 | 1758.98 | 0.0 | |
| M7 (beta) | 28 | −40929.27 | p = 0.706, q = 2.565 | ||||
| M8 (beta & w>1) | 30 | −40851.91 | p0 = 0.890, p = 1.182, q = 7.291, (p1 = 0.110), ω = 1.000 | M7 and M8 | 154.72 | 0.0 | None |
| Data set: fish | |||||||
| M0 (one ratio) | 41 | −54906.39 | ω = 0.309 | None | |||
| M1a (nearly neutral) | 42 | −53795.95 | p 0 = 0.683, (p 1 = 0.317) | ||||
| M2a (positive selection) | 44 | −53795.95 | p 0 = 0.683, p 1 = 0.265, (p 2 = 0.052), ω 2 = 1.00 | M2a and M1a | 0.0 | 1.0 | Not allowed |
| M3 (discrete) | 45 | −53584.70 | p 0 = 0.320, p 1 = 0.455, (p 2 = 0.225), ω0 = 0.058, ω 1 = 0.273, ω 2 = 0.987 | M3 and M0 | 2643.38 | 0.0 | |
| M7 (beta) | 42 | −53637.19 | p = 0.694, q = 1.342 | ||||
| M8 (beta & w>1) | 44 | −53562.02 | p0 = 0.864, p = 1.045, q = 3.305, (p1 = 0.136), ω = 1.197 | M7 and M8 | 150.34 | 0.0 | 293I, 294T, 432G, 433P, 737T, 802D, 1360S |
Note: the site models were conducted on mammalian or fish C3 gene sequences with two invertebrate C3 as out-group, respectively.
1
: only the sites with PP>0.95 were shown and those with PP>0.99 are in bold.
2
: this means that the models which allowed the positively selected sites exist in sequences did not pass the likelihood ratio test and thus the positively selected sites were not allowed to exist.