Table 4.
Likelihood ratio tests comparing models of molecular evolution of MAT genes
| Gene | Analysis | λ1 | df1 | 2Δλ1 | p-value | dN/dS | Parameters |
|---|---|---|---|---|---|---|---|
| MAT1-1-1 | M0: one ratio | -2205.4733 | 4 | 5.9586 | 0.2023 | 0.4280 | ω = 0.4280 |
| M3: discrete (κ = 3) | -2202.4940 | 0.4462 | p0 = 0.3732, ω0 = 0.7052; p1 = 0.3932, ω1 = 0.1117; p2 = 0.2336, ω2 = 0.7052 | ||||
| M1a: nearly neutral | -2202.6642 | 2 | 0.0000 | 1.0000 | 0.4599 | p0 = 0.6556, ω0 = 0.1761; p1 = 0.3440, ω1 = 1 | |
| M2a: positive selection | -2202.6642 | 0.4599 | p0 = 0.6556, ω0 = 0.1761; p1 = 0.2332, ω1 = 1; p2 = 0.1109, ω2 = 1 | ||||
| M7: β | -2202.5615 | 2 | 0.0000 | 1.0000 | 0.4507 | p0 = 0.4117; q = 0.5019 | |
| M8: β & ω > 1 | -2202.5615 | 0.4507 | p0 = 0.1000 p = 0.4117 q = 0.5019; (p1 = 0.00001) ω = 1.0000 | ||||
| MAT1-1-3 | M0: one ratio | -1706.3379 | 4 | 20.5175 | 0.0004* | 0.295 | ω = 0.2951 |
| M3: discrete (κ = 3) | -1696.0792 | 0.3103 | p0 = 0.0007, ω0 = 0.1116; p1 = 0.9232, ω1 = 0.1117; p2 = 0.0761, ω2 = 2.7212 | ||||
| M1a: nearly neutral | -1697.3663 | 2 | 2.5742 | 0.2761 | 0.2598 | p0 = 0.7402, ω0 = 0; p1 = 0.2598, ω1 = 1 | |
| M2a: positive selection | -1696.0792 | 0.3103 | p0 = 0.9239, ω0 = 0.1117; p1 = 0, ω1 = 1; p2 = 0.0761, ω2 = 2.7212 | ||||
| M7: β | -1697.6108 | 2 | 3.0594 | 0.2166 | 0.3000 | p = 0.0050; q = 0.0119 | |
| M8: β & ω > 1 | -1696.0811 | 0.3104 | p0 = 0.9244 p = 12.5791 q = 99.0000; (p1 = 0.0756) ω = 2.7290 | ||||
| MAT1-2-1 | M0: one ratio | -2133.8605 | 4 | 11.1677 | 0.0247* | 0.3714 | ω = 0.37135 |
| M3: discrete (κ = 3) | -2128.2767 | 0.4212 | p0 = 0.3531, ω0 = 0.2495; p1 = 0.6157, ω1 = 0.2496; p2 = 0.0312, ω2 = 5.7427 | ||||
| M1a: nearly neutral | -2129.6740 | 2 | 2.7948 | 0.2472 | 0.3528 | p0 = 0.6472, ω0 = 0; p1 = 0.3528, ω1 = 1 | |
| M2a: positive selection | -2128.2767 | 0.4212 | p0 = 0.9688, ω0 = 0.2496; p1 = 0, ω1 = 1; p2 = 0.0312, ω2 = 5.7428 | ||||
| M7: β | -2129.8169 | 2 | 3.0800 | 0.2144 | 0.3387 | p = 0.0170; q = 0.0321 | |
| M8: β & ω > 1 | -2128.2769 | 0.4212 | p0 = 0.9690 p = 33.0717 q = 99.0000; (p1 = 0.0310) ω = 5.7612 |
Models of neutral evolution (M1a and M7) are tested against models that incorporate positive selection (M2a and M8). Comparison of M0 vs. M3 tests variable dN/dS rate ratios among sites. Model M3 classifies sites in the sequence into discrete classes (κ = 3) with both the dN/dS rate ratio ω0, ω1, ω3 and the proportions p0, p2 and p3 estimated from the data. For models M1a and M2a, values of p0, p1, and p2, are the proportions of sites inferred to be evolving under purifying selection, neutral evolution, and positive selection, respectively, and ω0, ω1 and ω2 are their corresponding dN/dS rate ratios. For models M7 and M8, the β distribution, β (p, q), describes the distribution of the dN/dS rate ratio between zero and one, and p0 is the proportion of sites within this distribution. In these models, p1 is the proportion of sites inferred to be under positive selection, and ω is the dN/dS rate ratio for those sites.