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. 2017 Jun 30;8:1156. doi: 10.3389/fpls.2017.01156

Table 3.

Likelihood ratio test statistic and parameters estimated from the M3 and M3 + S1 models in Fitmodel.

Subfamily/COG M3 Modela (Heterogeneity across sites) M3 + S1 Model (Shifting across branches) Positive sites (M3 + S1 Model)
−ln L p1
ω1 		p2
ω2 		p3
ω3 		−ln L p1
ω1 		p2
ω2 		p3
ω3 		Dicots specific Grasses specific
Ia/NAM/CUC3
Ia_1 7,987.10 0.488 0.263 0.249 7,945.83** 0.587 0.231 0.181 153, 154, 159, 167 30, 172, 173, 177, 202
0.001 0.081 0.437 <0.001 0.103 0.671
Ia_2 8,695.22 0.505 0.305 0.191 8,617.30** 0.595 0.258 0.147 33, 155, 166, 170, 176, 177, 180 135, 161, 172, 173, 187, 188, 174, 175
0.014 0.225 0.957 <0.001 0.243 1.658
Ia_3 7,089.74 0.548 0.377 0.075 7,029.95** 0.614 0.308 0.079 136 120, 135
0.024 0.242 0.997 0.001 0.335 2.041
Ia_4 6,151.02 0.472 0.286 0.242 6,140.29** 0.513 0.246 0.241 11, 178, 185, 189, 208, 220, 245, 255 182, 207, 208, 228
0.009 0.235 0.925 0.003 0.207 1.096
Ia_5 5,945.22 0.518 0.233 0.249 5,903.54** 0.665 0.276 0.059 — 225
0.014 0.281 0.863 0.011 0.699 3.616
Ib/NAC1
Ib_1 7,286.55 0.498 0.202 0.299 7,241.32** 0.641 0.236 0.123 88, 193 94, 126, 141, 145, 170, 180, 183, 191
0.006 0.118 0.489 0.005 0.290 1.152
Ib_2 6,771.42 0.624 0.263 0.113 6,745.78** 0.671 0.261 0.068 155, 162 159, 181, 166, 178
0.013 0.274 0.906 0.006 0.350 2.233
Ic/SND
Ic_1 9,314.31 0.592 0.318 0.091 9,266.30** 0.735 0.221 0.044 163 145, 151
0.007 0.111 0.488 0.005 0.206 1.274
Ic_2 6,893.55 0.537 0.334 0.128 6,873.30** 0.589 0.282 0.129 — 167, 170, 176, 177, 202, 204
0.009 0.235 0.979 <0.001 0.240 1.193
Ic_3 5,718.94 0.682 0.243 0.075 5,711.67** 0.705 0.218 0.077 183 162, 164, 171
0.014 0.259 0.997 0.008 0.279 1.151
Ic_4 7,459.08 0.644 0.276 0.080 7,419.25** 0.732 0.120 0.068 144, 149, 169, 217 199, 200, 140, 142
0.012 0.237 1.088 0.009 0.369 1.728
Ic_5 5,286.13 0.520 0.224 0.257 5,272.27** 0.670 0.286 0.015 167 —
0.006 0.111 0.470 0.007 0.464 2.997
II/ONAC4
II_1 7,535.33 0.635 0.225 0.140 7,527.86** 0.670 0.203 0.128 16, 146, 207 —
0.009 0.187 0.738 0.005 0.204 0.867
II_2 7,642.77 0.227 0.498 0.235 7,606.47** 0.379 0.400 0.220 8, 11, 13, 14, 15, 16, 35, 67, 129, 145, 146, 202, 204, 205, 207, 208, 210 22, 31, 73, 144, 167, 225
0.009 0.225 0.784 <0.001 0.233 1.138
II_3 7,027.97 0.568 0.289 0.142 7,003.30** 0.621 0.211 0.168 2, 206, 227 58, 211, 212, 213
0.010 0.129 0.532 0.002 0.147 0.633
II_4 8,916.62 0.411 0.399 0.190 8,781.10** 0.673 0.285 0.042 249, 342 —
0.025 0.265 0.860 0.015 0.724 >>1
IIIa/TIP
IIIa_1 9,189.64 0.422 0.278 0.301 9,160.07** 0.496 0.293 0.211 161, 163, 165, 175 100, 159, 162, 187, 189, 195
0.007 0.137 0.589 0.002 0.186 0.852
IIIa_2 8,769.59 0.290 0.352 0.358 8,726.21** 0.349 0.315 0.337 171, 196, 219, 226, 230, 231, 238 157, 158, 222, 234, 236, 239, 241
0.006 0.113 0.615 0.002 0.101 0.781
IIIb/NAC2
IIIb_1 11,715.75 0.666 0.309 0.025 11,609.68** 0.685 0.266 0.049 127 92
0.010 0.109 0.562 0.002 0.123 0.614
IIIb_2 9,955.97 0.298 0.342 0.360 9,913.68** 0.548 0.240 0.211 183, 201, 203, 213, 218, 238 176, 185,196, 200, 204, 215
0.011 0.133 0.682 0.023 0.315 1.233
IIIb_3 11,351.55 0.327 0.337 0.336 11,319.73** 0.408 0.281 0.311 4, 176, 177, 179, 201, 250, 259, 280, 337, 339 —
0.016 0.218 0.717 0.006 0.242 0.885
IIIc/ANAC11 5,331.14 0.482 0.337 0.180 5,280.02** 0.578 0.246 0.176 2, 98, 110, 162, 176, 178, 181, 183, 152, 162, 163 150, 153, 154, 155, 158, 160, 165, 168, 169, 170, 173, 174, 177, 184
0.007 0.160 1.051 <0.001 0.157 1.613
IVb/ANAC34
IVb_1 7,232.44 0.587 0.238 0.174 7,188.84** 0.655 0.209 0.136 190, 191, 192 2, 172, 196, 197, 201
0.011 0.224 0.823 0.002 0.218 1.324
IVb_2 6,123.96 0.404 0.399 0.197 6,086.42** 0.583 0.286 0.131 1, 3, 176 157, 163, 185
0.003 0.122 0.587 <0.001 0.188 1.137
IVc/TERN 7,932.92 0.581 0.298 0.121 7,898.20** 0.641 0.260 0.098 149 42
0.038 0.400 1.115 0.021 0.487 1.628
IVd/ONAC22
IVd_1 9,087.07 0.483 0.267 0.250 9,072.53** 0.520 0.255 0.226 181, 187, 197, 210, 220, 234 178, 179, 183, 199, 206, 213, 229
0.007 0.167 0.711 0.002 0.173 0.834
IVd_2 7,912.34 0.535 0.279 0.186 7,896.29** 0.605 0.272 0.123 143, 50, 126, 146, 147, 148, 149, 150, 154 153, 158
0.006 0.152 0.717 0.002 0.191 1.026
Va/NAP
Va_1 6,872.05 0.488 0.308 0.204 6,833.05** 0.566 0.285 0.148 95, 150, 156, 184, 185, 186, 187, 190, 191, 201, 205, 209 162, 164, 197, 206, 208
0.007 0.239 1.030 <0.001 0.335 1.746
Va_2 6,093.17 0.466 0.282 0.252 6,066.48** 0.544 0.252 0.203 116, 148, 150, 195, 196, 201 163, 191, 202, 208, 133, 156, 158, 159, 209
0.006 0.177 0.892 0.004 0.253 1.260
Vb/SNAC_11 15,736.23 0.594 0.229 0.177 15,647.48** 0.612 0.222 0.165 52 28, 47, 50, 80, 115, 148, 151, 152
0.003 0.067 0.233 <0.001 0.054 0.349
VIc/ONAC6 6,176.96 0.382 0.533 0.086 6,159.23** 0.525 0.428 0.046 114 82
0.027 0.262 0.887 0.006 0.395 2.033
a

pi proportion of sites that fall into the ωi site class, i = 1, 2, 3.

**

P < 0.01, and the probabilities are obtained by LRT (df = 2) of the models M3 and M3 + S1.