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Table 4 Positive selective amino acid loci and estimation of parameters for fourteen genes in subfamily Zingiberoideae

From: Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

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*
  1. Note: the degree of freedom for each gene was 38; * and ** indicate posterior probability higher than 0.95 and 0.99, respectively