Table 4.
Parameter estimates and likelihood scores for branch- site models for 5 species
| Species | Model | l (1) | Estimates of parameters (2) | 2Δl (3) | Positively selected sites (BEB) |
|---|---|---|---|---|---|
| Marmoset | Null | -5660.37202 | ρ0 = 0.18, (ρ1 = 0.39), ω0 = 0.23, (ω1 = 1) | 18.47 *** | Not allowed |
| Alternative | -5651.1375 | ρ0 = 0.30, ρ1 = 0.63, (ρ2 = 0.07), ω0 = 0.23, (ω1 = 1), ω2 = 60.38 | 2 sites p > 95%: 159R, 161F | ||
| Dog | Null | -5660.55998 | ρ0 = 0.25, (ρ1 = 0.52), ω0 = 0.24, (ω1 = 1) | 6.78 ** | Not allowed |
| Alternative | -5657.16845 | ρ0 = 0.28, ρ1 = 0.58, (ρ2 = s0.14), ω0 = 0.23, (ω1 = 1), ω2 = 11.15 | 2 sites p > 95%: 14H, 144Y | ||
| Guinea pig | Null | -5660.94116 | ρ0 = 0.32, (ρ1 = 0.67), ω0 = 0.24, (ω1 = 1) | 13.68 *** | Not allowed |
| Alternative | -5654.10045 | ρ0 = 0.27, ρ1 = 0.51, (ρ2 = 0.22), ω0 = 0.25, (ω1 = 1), ω2 = 3.94 | 3 sites p > 95%: 11S, 75C, 104V | ||
| Horse | Null | -5660.94121 | ρ0 = 0.32, (ρ1 = 0.67), ω0 = 0.24, (ω1 = 1 ) | 27.22 *** | Not allowed |
| Alternative | -5647.32999 | ρ0 = 0.30, ρ1 = 0.61, (ρ2 = 0.09), ω0 = 0.24, (ω1 = 1), ω2 = 7.57 | 2 sites p > 99%: 75C, 119L; 1 site p > 95%: 144Y | ||
| Mouse | Null | -5658.60187 | ρ0 = 0.24, (ρ1 = 0.55), ω0 = 0.19, (ω1 = 1 ) | 10.75 ** | Not allowed |
| Alternative | -5653.22783 | ρ0 = 0.25, ρ1 = 0.58, (ρ2 = 0.17), ω0 = 0.19, (ω1 = 1), ω2 = 3.25 | 1 site p > 95%: 162Q | ||
(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 < 0.01
*** significant at p < 0.001.
(4) Underlined: amino acids involved in androstenol and androstenone binding.
Site numbers and amino acids refer to the pig SAL1 reference sequence PDB: 1GM6, except for the amino acid in bold, which is not part of the structure but comes from the dog genome sequence XP_855342.1.