TABLE 2.
Model comparisons for primate sequences
| Models compared | −2ΔlnL | Parameter estimates under selection model | Positively selected sites |
|---|---|---|---|
| Neutral (M1) vs. selection (M2) | 35.04** | p1 = 0.96, ω1 = 0.51 | 64, 68, 102, 110, 139, 146, 190, 257, 278, 337, 341, 354, 361, 426, 431, 525, 623, 644, 665, 672, 743, 846, 1056 |
| (d.f. = 2) | p2 = 0, ω2 = 1.00 | ||
| p3 = 0.04, ω3 = 6.76 | |||
| One-ratio (M0) vs. discrete (M3) | 63.22** | p1 = 0.33, ω1 = 0.51 | 64, 68, 102, 110, 139, 146, 190, 257, 278, 337, 341, 354, 361, 426, 431, 525, 587, 623, 639, 640, 644, 665, 672, 743, 760, 846, 1056 |
| (d.f. = 4) | p2 = 0.63, ω2 = 0.51 | ||
| p3 = 0.04, ω3 = 6.76 | |||
| β (M7) vs. β and ω (M8) | 35.06** | p0 = 0.96, p = 99.0, q = 93.2 | 64, 68, 102, 110, 139, 146, 190, 257, 278, 337, 341, 354, 361, 426, 431, 525, 587, 623, 639, 640, 644, 665, 672, 743, 760, 846, 1056 |
| (d.f. = 2) | (p1 = 0.044) | ||
| ω = 6.80 | |||
| β and ω = 1 (M8a) vs. β and ω (M8) | 17.52** | Same as above | Same as above |
| (d.f. = 1) | |||
| One-ratio (M0) vs. free-ratio | 25.55 | NA | NAa |
| (d.f. = 20) | |||
| Branch site neutral vs. selection | 43.17** | p0 = 0.395, ωbg = 0.030, ωfg = 0.030 | 102, 257, 672, 1056 |
| (d.f. =1) | p1 = 0.601 ωbg = 1.00, ωfg = 1.00 | ||
| p2a = 0.001, ωbg = 0.030, ωfg = 999 | |||
| p2b = 0.002, ωbg = 1.00, ωfg = 999 |
Boldface type indicates sites that have a prediction of P > 90% based on Bayes empirical Bayes. Italic type indicates sites that have a prediction of P > 80%. Underlining indicates sites that have a prediction of P > 70%. **Significant P < 0.001.
a
The test is not significant in our data set; therefore, we do not display the values from the free ratio.