Table 5 The potential positive selection test based on the branch-site model
Gene | Null hypothesis | Alternative hypothesis | Significance test | |||||
|---|---|---|---|---|---|---|---|---|
name | lnL | df | Omega (w = 1) | lnL | df | Omega (w > 1) | BEB | P-value |
accD | − 6244.2703 | 76 | 1 | − 6251.82 | 75 | 40.32412 | 78 I 0.946,79 D 0.840,80 S 0.573,81 G 0.779,82 K 0.969*,87 G 0.750,90 D 0.597,148 M 0.565,157 H 0.557,162 P 0.654,167 I 0.715,188 N 0.626,208 S 0.753,262 N 0.683,295 N 0.585,314 V 0.694 | 1.01E-04 |
atpA | − 7235.2876 | 80 | 1 | −7235.29 | 79 | 1 | 123 V 0.784 | 9.99E-01 |
atpB | − 6617.3383 | 80 | 1 | −6617.34 | 79 | 1.00000 |  | 1.00E+ 00 |
atpE | −2016.8158 | 80 | 1 | −2018 | 79 | 87.46955 | 35 P 0.917,52 Y 0.977* | 1.23E-01 |
atpF | − 857.07265 | 80 | 1 | −857.073 | 79 | 1.00000 |  | 1.00E+ 00 |
atpH | − 800.09979 | 76 | 1 | −800.1 | 75 | 3.48674 |  | 9.98E-01 |
atpI | − 3183.0473 | 80 | 1 | −3183.51 | 79 | 20.22025 | 35 V 0.753,59 R 0.824,96 P 0.843,202 V 0.828 | 3.38E-01 |
ccsA | − 5988.5949 | 80 | 1 | − 5989.75 | 79 | 15.32850 | 14 S 0.673,120 I 0.887 | 1.28E-01 |
cemA | − 4097.1783 | 79 | 1 | −4097.63 | 78 | 999.00000 |  | 3.41E-01 |
clpP | − 3779.5729 | 78 | 1 | −3779.64 | 77 | 1.73510 | 16 D 0.577,80 F 0.508,88 T 0.606,93 V 0.593,95 I 0.548 | 7.05E-01 |
matK | − 9319.3607 | 80 | 1 | −9319.36 | 79 | 1.00000 |  | 1.00E+ 00 |
ndhA | − 5632.3781 | 78 | 1 | −5632.38 | 77 | 1.00000 |  | 1.00E+ 00 |
ndhC | − 1481.7425 | 79 | 1 | −1481.74 | 78 | 1.00000 |  | 9.99E-01 |
ndhD | − 6748.038 | 78 | 1 | −6748.06 | 77 | 1.50673 | 63 M 0.697,201 I 0.662,252 I 0.664,320 L 0.685,327 Y 0.714,356 I 0.712 | 8.29E-01 |
ndhE | − 1550.4989 | 80 | 1 | −1550.5 | 79 | 1.00000 |  | 1.00E+ 00 |
ndhF | −14,465.344 | 76 | 1 | −14,465.3 | 75 | 1.00000 | 116 A 0.557,280 I 0.550 | 1.00E+ 00 |
ndhG | − 2862.0535 | 79 | 1 | −2862.05 | 78 | 1.00000 |  | 1.00E+ 00 |
ndhH | − 5898.3248 | 78 | 1 | −5898.32 | 77 | 1.00000 | 318 T 0.527 | 1.00E+ 00 |
ndhI | − 2246.7819 | 78 | 1 | − 2247.13 | 77 | 13.49799 | 49 T 0.845,88 D 0.585,96 N 0.815 | 4.02E-01 |
ndhJ | − 2064.866 | 80 | 1 | −2064.87 | 79 | 1.00000 | 134 G 0.745 | 1.00E+ 00 |
ndhK | − 2624.0218 | 76 | 1 | −2624.02 | 75 | 1.00000 | 161 Y 0.548 | 1.00E+ 00 |
petA | − 2607.1562 | 80 | 1 | −2607.16 | 79 | 10.70011 |  | 9.89E-01 |
petG | − 404.32829 | 80 | 1 | −404.369 | 79 | 1.00000 |  | 7.76E-01 |
petL | − 386.63805 | 80 | 1 | − 385.507 | 79 | 1.41918 |  | 1.33E-01 |
petN | −218.82071 | 80 | 1 | −218.821 | 79 | 3.96657 |  | 9.95E-01 |
psaA | − 7414.7714 | 80 | 1 | −7414.77 | 79 | 1.15065 | 441 V 0.583 | 9.85E-01 |
psaB | − 7487.909 | 80 | 1 | −7487.91 | 79 | 1.00000 | 177 L 0.522 | 9.86E-01 |
psaC | −965.2544 | 80 | 1 | −965.254 | 79 | 1.00000 |  | 9.99E-01 |
psaI | −489.20384 | 80 | 1 | −489.204 | 79 | 1.00000 | 22 A 0.857 | 9.94E-01 |
psaJ | − 623.17909 | 80 | 1 | − 622.516 | 79 | 1.00000 |  | 2.50E-01 |
psbA | −3805.4481 | 80 | 1 | −3805.45 | 79 | 1.00000 | 3 A 0.784,228 T 0.784,350 S 0.738 | 1.00E+ 00 |
psbC | − 5464.4744 | 80 | 1 | −5464.47 | 79 | 1.00000 |  | 1.00E+ 00 |
psbD | − 3430.3571 | 80 | 1 | −3430.36 | 79 | 1.00000 |  | 9.89E-01 |
psbE | −824.21551 | 80 | 1 | −824.216 | 79 | 1.00000 |  | 1.00E+ 00 |
psbF | − 297.73519 | 80 | 1 | −297.735 | 79 | 1.00000 |  | 1.00E+ 00 |
psbI | −386.8387 | 80 | 1 | −386.839 | 79 | 1.00000 |  | 1.00E+ 00 |
psbJ | −409.58353 | 80 | 1 | −409.584 | 79 | 3.05096 |  | 9.99E-01 |
psbK | − 808.36136 | 80 | 1 | −808.361 | 79 | 1.00000 |  | 1.00E+ 00 |
psbL | −251.14656 | 80 | 1 | −250.996 | 79 | 1.00000 |  | 5.83E-01 |
psbM | −344.18423 | 80 | 1 | −344.184 | 79 | 1.00000 |  | 1.00E+ 00 |
psbN | −339.98529 | 78 | 1 | −339.985 | 77 | 3.88417 |  | 1.00E+ 00 |
psbZ | −615.4539 | 76 | 1 | −615.454 | 75 | 1.00000 | 17 L 0.553 | 1.00E+ 00 |
rbcL | − 6385.4416 | 80 | 1 | − 6388.64 | 79 | 999.00000 | 365 L 0.908 | 1.14E-02 |
rpl20 | − 2104.3884 | 80 | 1 | −2104.39 | 79 | 1.00000 |  | 1.00E+ 00 |
rpl33 | − 895.54775 | 80 | 1 | −895.771 | 79 | 84.08315 | 57 G 0.873 | 5.04E-01 |
rpoA | − 5786.0327 | 76 | 1 | −5786.03 | 75 | 1.00000 | 5 A 0.523,107 Y 0.502,125 S 0.554,135 Q 0.559,276 K 0.555 | 1.00E+ 00 |
rpoB | −14,722.031 | 80 | 1 | −14,722 | 79 | 1.24476 | 281 A 0.535,454 Y 0.537 | 9.55E-01 |
rpoC1 | − 9096.3909 | 78 | 1 | −9096.39 | 77 | 1.00000 | 110 A 0.561,590 P 0.569 | 1.00E+ 00 |
rpoC2 | −21,869.149 | 80 | 1 | −21,869.1 | 79 | 1.00000 |  | 9.99E-01 |
rps14 | − 1369.7427 | 78 | 1 | − 1370.22 | 77 | 999.00000 | 28 R 0.844,35 L 0.559 | 3.29E-01 |
rps15 | −324.00056 | 74 | 1 | −323.269 | 73 | 2.04455 |  | 2.26E-01 |
rps18 | − 1134.1501 | 80 | 1 | −1134.15 | 79 | 1.00000 |  | 1.00E+ 00 |
rps2 | − 3349.317 | 80 | 1 | −3349.32 | 79 | 1.00000 | 124 E 0.631,182 I 0.648 | 1.00E+ 00 |
ycf3 | − 1601.2056 | 78 | 1 | −1601.35 | 77 | 24.41198 | 5 R 0.733 | 5.89E-01 |
ycf4 | − 2660.8473 | 79 | 1 | − 2661.13 | 78 | 71.02868 |  | 4.55E-01 |