Table 2.
Parameter estimates and likelihood scores for branch-site models for paralogs
| Genes | Model | l (1) | Estimates of parameters (2) | 2Δl (3) | Positively selected sites (BEB) |
|---|---|---|---|---|---|
| Cow LOC783399 | Null | -5660.941163 | ρ0 = 0.32, (ρ1 = 0.68), ω0 = 0.24, (ω1 = 1) | 27.10 *** | Not allowed |
| Alternative | -5647.392083 | ρ0 = 0.30, ρ1 = 0.66, (ρ2 = 0.05), ω0 = 0.23, (ω1 = 1), ω2 = ∞ | 1 site p > 99%: 36Y | ||
| Guinea pig ENSCPOG00000023399 | Null | -5660.050892 | ρ0 = 0.25, (ρ1 = 0.50), ω0 = 0.24, (ω1 = 1) | 56.40 *** | Not allowed |
| Alternative | -5631.851037 | ρ0 = 0.27, ρ1 = 0.55, (ρ2 = 0.18), ω0 = 0.23, (ω1 = 1), ω2 = 336.70 | 7 sites p > 99%: 24R, 27A, 113L, 118Q, 123T, 125T, 128T, 8 sites p > 95%: 31L, 25E, 26T, 85V, 114T, 117T, 122V, 126L | ||
| Horse LOC100053653 | Null | -5665.171131 | ρ0 = 0.22, (ρ1 = 0.47), ω0 = 0.23, (ω1 = 1) | 15.86 *** | Not allowed |
| Alternative | -5657.239232 | ρ0 = 0.09, ρ1 = 0.19, (ρ2 = 0.72), ω0 = 0.23, (ω1 = 1), ω2 = 6.44 | 6 sites p > 95%: 81E, 97A, 123Q, 135K, 166K, 168F | ||
| Mouse Mup19 | Null | -5660.941163 | ρ0 = 0.32, (ρ1 = 0.67), ω0 = 0.24, (ω1 = 1) | 53.87 *** | Not allowed |
| Alternative | -5634.004112 | ρ0 = 0.30, ρ1 = 0.66, (ρ2 = 0.04), ω0 = 0.23, (ω1 = 1), ω2 = ∞ | 2 sites p > 99%: 174K, 177F | ||
| Rat LOC298116 | Null | -5660.941163 | ρ0 = 0.32, (ρ1 = 0.67), ω0 = 0.24, (ω1 = 1) | 8.69 *** | Not allowed |
| Alternative | -5656.597218 | ρ0 = 0.32, ρ1 = 0.66, (ρ2 = 0.02), ω0 = 0.24, (ω1 = 1), ω2 = ∞ | 1 site p > 99%: 135A | ||
(1) Log- likelihood values.
(2) ρ0, ρ1, and ρ2 are the proportions of codons subject to purifying selection, neutral evolution, and positive selection, respectively. ω0, ω1 and ω2 represented dN/dS for each class (purifying, neutral and positive selection, respectively).
(3) *** significant at p < 0.001.