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Table 2 Likelihood values and parameter estimates for the OPR genes in plants

From: Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

Models P a dN/dSb Estimates of parametersc 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
  1. a Number of parameters in the ω distribution.
  2. b The dN/dS ratio is an average over all sites of OPR gene alignments.
  3. c Parameters in parentheses are not free parameters.
  4. 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.
  5. * The amino acid residues depicted with an asterisk were also found to be implicated in the functional divergence between OPR paralogues (see Table 3).