Table 4.
Positive selective amino acid loci and estimation of parameters for fourteen genes in subfamily Zingiberoideae
| Gene | Ln L | Estimates of parameters | Positively selected sites |
|---|---|---|---|
| accD | −2726.384456 |
p0 = 0.96351 p = 0.00502 q = 0.00512 (p1 = 0.003649) ω = 11.82130 |
4 W 1.000**, 9 L 0.987*, 218H 0.958*, 299R 0.968* |
| ccsA | − 1712.097311 |
p0 = 0.97744 p = 0.00507 q = 0.02055 (p1 = 0.02256) ω = 13.95433 |
87 T 0.957*, 180 L 0.994**, 200Y 1.000**, 201 K 1.000** |
| ndhA | − 1991.585023 |
p0 = 0.98899 p = 0.01051 q = 0.03386 (p1 = 0.01101) ω = 57.72615 |
132F 0.964*, 189S 1.000**, 190S 1.000**, 191 T 1.000**, 192 V 1.000** |
| ndhB | − 2119.544926 |
p0 = 0.98391 p = 0.00500 q = 13.07861 (p1 = 0.01609) ω = 43.84612 |
133 V 0.953*, 181 T 0.957*, 246P 0.955* |
| psbJ | −162.569004 |
p0 = 0.97242 p = 0.00500 q = 18.09039 (p1 = 0.02758) ω = 999.00000 |
20 L 1.000** |
| rbcL | − 2346.044248 |
p0 = 0.97658 p = 0.01215 q = 0.20915 (p1 = 0.02342) ω = 14.08875 |
169 L 0.980*, 225I 0.996**, 226Y 0.997**, 247C 0.963*, 255I 0.955*, 407 L 0.980*, 424 L 0.999**, 449S 1.000** |
| rpl20 | −806.763954 |
p0 = 0.94834 p = 0.00500 q = 0.01576 (p1 = 0.05166) ω = 8.41059 |
118 K 0.998**, 125Y 1.000** |
| rpoC1 | − 3213.853612 |
p0 = 0.98613 p = 33.03585 q = 99.00000 (p1 = 0.01387) ω = 11.40945 |
147 N 0.972*, 606D 0.971* |
| rpoC2 | − 6806.754011 |
p0 = 0.98887 p = 0.04146 q = 0.09596 (p1 = 0.01113) ω = 11.89405 |
711Y 0.995**, 1174 W 0.984* |
| rps12 | − 759.324938 |
p0 = 0.73184 p = 17.58063 q = 0.00500 (p1 = 0.26816) ω = 772.95793 |
1 M 0.955*, 2P 0.996**, 3 T 0.961*, 4I 0.956*, 5 K 0.956*, 6Q 1.000**, 7 L 0.998**, 8I 0.999**, 9R 0.974*, 10 N 0.999**, 11A 0.998**, 12R 0.959*, 13Q 1.000**, 14P 0.966*, 15I 0.989*, 16R 0.959*, 17 N 0.999**, 18 V 0.999**, 19 T 1.000**, 20 K 1.000**, 21S 0.998**, 22P 0.998**, 23A 0.963*, 24 L 0.998**, 25R 0.986*, 26E 0.998**, 27C 0.964*, 28P 0.998**, 29Q 1.000**, 30R 0.998**, 31R 0.999**, 32G 0.999**, 33 T 0.999**, 34C 0.962*, 35 T 0.956*, 36R 0.958*, 37 V 0.998**, 38Y 0.960*, 94R 0.952*, 116Q 0.952* |
| rps18 | − 553.014018 |
p0 = 0.98952 p = 55.09674 q = 99.00000 (p1 = 0.01048) ω = 49.80264 |
27P 0.973* |
| ycf1 | −10,584.294185 |
p0 = 0.88238 p = 40.44610 q = 56.04336 (p1 = 0.11762) ω = 7.72414 |
14 L 0.994**, 16 M 0.985*, 48R 0.961*, 142 L 0.990**, 212A 0.989*, 215R 0.981*, 606D 0.975*, 663R 0.994**, 809Y 0.952*, 928P 0.992**, 1293 V 0.986*, 1302I 0.964*, 1341 M 1.000**, 1433 K 0.992**, 1439 N 0.999**, 1452 K 0.984*, 1453 K 0.982*, 1466 K 0.999**, 1469S 0.998**, 1473D 0.999**, 1499D 0.966*, 1506Q 0.991**, 1528E 0.988*, 1576F 0.990**, 1586Y 1.000**, 1590 K 0.990**, 1604P 0.990**, 1621A 0.987*, 1628 L 0.991**, 1629 N 0.993**, 1632D 0.993**, 1651G 0.987*, 1667S 0.995**, 1757 L 0.961* |
| ycf2 | −10,373.971098 |
p0 = 0.93261 p = 0.10353 q = 0.15548 (p1 = 0.06739) ω = 20.73253 |
220P 0.993**, 998D 0.993**, 1069I 0.993**, 1324 L 0.994**, 1343F 1.000**, 1411S 0.993**, 1665I 0.993**, 1758R 0.993**, 1977A 0.993**, 2121D 0.999**, 2191R 0.994**, 2261 L 0.963*, 2263H 0.993**, 2265 T 0.999**, 2266G 0.995**, 2267E 0.993**, 2268R 0.993**, 2269F 0.999**, 2271I 0.993**, 2272P 0.994** |
| ycf4 | −960.017298 |
p0 = 0.91059 p = 0.00500 q = 1.92107 (p1 = 0.08941) ω = 4.34827 |
181 M 0.962*, 184 L 0.971* |
Note: the degree of freedom for each gene was 38; * and ** indicate posterior probability higher than 0.95 and 0.99, respectively