Table 2.
Likelihood values and parameter estimates for the OPR genes in plants
| Models | Pa | dN/dSb | Estimates of parametersc | ℓ | Positively Selected Sitesd |
| M0 (one-ratio) |
1 | 1.047 | ω = 1.047 | -24650.04 | None |
| M1a (nearly neutral) |
2 | 0.649 | p0 = 0.415, (p1 = 0.585) ω0 = 0.154, ω1 = 1 | -23834.20 | Not allowed |
| M2a (positive selection) |
4 | 1.377 | p0 = 0.271, p1 = 0.447, (p2 = 0.283) ω0 = 0.113, ω1 = 1, ω2 = 3.183 | -23430.45 | 20, 22, 24, 35*, 39, 40*, 48, 51, 56*, 62*, 69*, 70*, 76, 83*, 102, 131, 132, 135, 151, 152, 157*, 158*, 163*, 170, 177, 205*, 207*, 227*, 228*, 233, 243*, 246, 248*, 249, 254*, 258*, 262, 267, 268, 301, 302, 303, 304, 305, 307*, 311, 314*, 319, 324*, 327*, 330*, 333, 334, 336, 345, 354, 357, 358, 359, 361 |
| M3 (discrete) |
5 | 1.414 | p0 = 0.274, p1 = 0.449, (p2 = 0.227) ω = 0.119, ω1 = 1.049, ω2 = 3.290 | -23430.13 | 16, 20, 22, 24, 35*, 39, 40*, 41*, 48, 51, 56*, 62*, 66, 69*, 70*, 76, 83*, 98, 102, 131, 132, 135, 151, 152, 157*, 158*, 159, 163*,170, 177, 205*, 207*, 223, 224, 227*, 228*, 233, 243*, 245, 246, 248*, 249, 254*, 258*, 262, 267, 268, 301, 302, 303, 304, 305, 307*, 311, 314*, 319, 324*, 325, 327*, 330*, 333, 334, 336, 345, 354, 357, 358, 359, 361 |
| M7 (beta) |
2 | 0.593 | p = 0.384, q = 0.264 | -23749.95 | Not allowed |
| M8 (beta &ω) |
4 | 1.194 | p0 = 0.733, (p1 = 0.267) p = 0.378, q = 0.264, ω = 2.853 | -23413.00 | 20, 22, 24, 35*, 39, 40*, 48, 51, 56*, 62*, 69*,70*, 76, 83*, 102, 131, 132, 135, 151, 152, 157*, 158*, 163*, 170, 177, 205*, 207*, 227*, 228*, 243*, 246, 248*, 249, 254*, 262, 267, 268, 301, 302, 303, 304, 305, 307*, 311, 314*, 319, 324*, 327*, 330*, 333, 334, 336, 345, 354, 357, 358, 359, 361 |
a Number of parameters in the ω distribution.
b The dN/dS ratio is an average over all sites of OPR gene alignments.
c Parameters in parentheses are not free parameters.
d Numbering of amino acid residues corresponds to AtOPR02-1(AtOPR3). Positive-selection sites are inferred at posterior probabilities >95% with those reaching 99% shown in bold. The lists of sites are identical between Naive Empirical Bayes (NEB) and Bayes Empirical Bayes (BEB) analysis in M2a and M8, while only Naive Empirical Bayes (NEB) analysis was used in M3.
* The amino acid residues depicted with an asterisk were also found to be implicated in the functional divergence between OPR paralogues (see Table 3).