TABLE 2.
Tests for selection among codons of SRY in Felidae using models implemented in PAML 315 using the likelihood method (see materialsandmethods)
| Criteria | Model | Parameter estimates | Ln likelihood | LRT | Selected codon, BEB posterior probabilitya |
|---|---|---|---|---|---|
| Among | M0 | κ = 2.11751 | −1624.383 | NA | NA |
| sites | (one ratio) | ω0 = 0.81556 | |||
| M1a | κ = 2.04609 | −1623.179 | NA | NA | |
| (nearly neutral) | ω0 = 0.21097 (p0 = 0.38216) | ||||
| ω1 = 1.00000 (p1 = 0.61784) | |||||
| M2a | κ = 2.11857 | −1619.815 | M2a vs. M1a | R46G (0.829) | |
| (selection) | ω0 = 0.63684 (p0 = 0.95861) | 6.729, P = 0.034, 2 d.f. | G47S (0.910) | ||
| ω1 = 1 (p1 = 0) | K125R (0.736) | ||||
| ω2 = 5.98942 (p2 = 0.04139) | D144E (0.569) | ||||
| M187V, L (0.656) | |||||
| M7 | κ = 2.06047 | −1623.196 | NA | NA | |
| (β-distribution, neutral) | β-distribution | ||||
| p = 0.13573, q = 0.03540 | |||||
| M8 | κ = 2.11873 | −1619.819 | M8 vs. M7 | R46G (0.870) | |
| (β-distribution, selection) | ωs = 5.99456 (p1 = 0.04130) | 6.754, P = 0.034, 2 d.f. | G47S (0.940) | ||
| β-distribution | K125R (0.815) | ||||
| p0 = 0.95870, p = 99.0, q = 56.358 | D144E (0.694) | ||||
| M187V, L (0.759) | |||||
| Y223H, C (0.588) | |||||
| M8a | κ = 2.04630 | −1623.181 | M8 vs. M8a | NA | |
| (β-distribution, ω = 1, fixed) | ω1 = 1.00000 (p1 = 0.61804) | 6.724, P = 0.0047, 1 d.f. | |||
| β-distribution | |||||
| p0 = 0.38196, p = 26.636, q = 99.0 |
P, proportion of sites; κ, transition:transversion ratio; ω = dN/dS for each proportion of sites; NA, not applicable;
a
Corresponding codon (see Figure 1) of 36-species alignment.