Table 3.
Positive selective amino acid loci and estimation of parameters
| Gene | Ln L | Estimates of parameters | Positively selected sites |
|---|---|---|---|
| ccsA | − 1688.900532 |
p0 = 0.99053p = 0.00799q = 0.00500 (p1 = 0.00947)ω = 122.48812 |
200 F 0.999**, 201 I 0.986* |
| clpP | − 1189.046814 |
p0 = 0.91790p = 0.02800q = 0.01097 (p1 = 0.08210)ω = 22.05525 |
22 E 0.966*, 24 Y 1.000**, 39 K 0.972*, 40 E 0.969*, 58 Q 0.979*, 72 W 0.979*, 75 S 0.998**, 78 A 0.960*, 120 V 1.000**, 153 T 0.975*, 192 L 0.961*, 204 L 0.953* |
| ndhA | − 1741.334638 |
p0 = 0.98308p = 12.72091q = 99.00000 (p1 = 0.01692)ω = 52.52860 |
132 S 0.996**, 189 R 1.000**, 190 V 1.000**, 191 I 0.998**, 192 L 0.998** |
| ndhB | − 2096.337425 |
p0 = 0.98968p = 0.00500q = 1.58164 (p1 = 0.01032)ω = 999.00000 |
133 I 0.995**, 145 G 0.951*, 181 T 0.995** |
| petD | − 753.029169 |
p0 = 0.96547p = 0.00500q = 1.79217 (p1 = 0.03453)ω = 7.43965 |
8 I 0.970* |
| psaA | − 3396.235357 |
p0 = 0.99301p = 0.00500q = 0.75911 (p1 = 0.00699)ω = 41.45919 |
261 F 0.999**, 292 A 0.981* |
| psbB | − 2254.262995 |
p0 = 0.99605p = 0.00500q = 1.52674 (p1 = 0.00395)ω = 373.49395 |
488 A 1.000** |
| psbC | − 2130.498976 |
p0 = 0.99356p = 0.00500q = 1.59626 (p1 = 0.00644)ω = 85.67788 |
24 T 0.970*, 280 S 0.978* |
| rbcL | − 2275.465641 |
p0 = 0.96928p = 0.48224q = 5.55236 (p1 = 0.03072)ω = 24.32347 |
19 G 0.992**, 30 T 0.999**, 176 L 0.988*, 232 L 1.000**, 233 F 1.000**, 254 C 0.981*, 269 T 0.970*, 289 H 0.998**, 333 I 0.998**, 431 L 0.987*, 456 S 1.000** |
| rpl12 | − 1180.117502 |
p0 = 0.99203p = 0.00500q = 3.98754 (p1 = 0.00797)ω = 77.23012 |
140 S 0.966* |
| rpl20 | − 745.824555 |
p0 = 0.95179p = 0.00871q = 0.02374 (p1 = 0.04821)ω = 35.61813 |
120 S 1.000**, 121 N 1.000**, 122 K 1.000**, 123 V 1.000**, 124 H 1.000** |
| rpl23 | −430.542995 |
p0 = 0.97858p = 0.00500q = 2.07543 (p1 = 0.02142)ω = 999.00000 |
57 E 0.976* |
| rpl33 | − 288.922817 |
p0 = 0.00001p = 0.00500q = 2.19296 (p1 = 0.99999)ω = 999.00000 |
3 K 0.988*, 6 D 0.988*, 29 G 0.988*, 42 M 0.988*, 43 P 0.988* |
| rpoC2 | − 6439.688674 |
p0 = 0.99492p = 0.04204q = 0.16546 (p1 = 0.00508)ω = 22.05755 |
593 D 0.978*, 743 P 0.985*, 1181 W 0.986* |
| rps7 | − 698.656393 |
p0 = 0.98065p = 0.00500q = 1.44246 (p1 = 0.01935)ω = 485.63912 |
81 G 0.966* |
| rps12 | −575.913647 |
p0 = 0.99188p = 0.01544q = 0.03483 (p1 = 0.00812)ω = 999.00000 |
116 Q 0.958* |
| ycf1 | −10,914.54603 |
p0 = 0.70387p = 0.00500q = 1.91338 (p1 = 0.29613)ω = 7.28992 |
14 S 0.996**, 16 I 0.990*, 48 R 0.970*, 65 I 0.994**, 315 R 0.958*, 353 R 0.977*, 384 S 0.961*, 404 L 0.994**, 464 E 0.952*, 588 N 0.997**, 598 F 0.994**, 622 E 0.990*, 682 L 0.953*, 684 A 0.994**, 699 H 0.994**, 705 Q 0.996**, 728 S 1.000**, 729 V 0.997**, 748 Q 0.996**, 753 R 1.000**, 861 I 0.998**, 869 L 0.961*, 883 L 0.965*, 900 Y 0.972*, 905 E 0.951*, 936 T 0.991**, 944 L 0.952*, 982 T 0.960*, 991 A 0.968*, 1027 P 0.991**, 1339 R 0.996**, 1449 R 0.997**, 1538 I 0.995**, 1539 S 0.996**, 1547 H 0.990**, 1564 S 1.000**, 1568 W 0.979*, 1569 S 0.977*, 1597 F 0.962*, 1657 T 0.991**, 1671 P 0.965*, 1672 L 0.956*, 1690 S 0.996**, 1695 L 0.953*, 1713 I 0.994**, 1715 H 0.993**, 1719 R 0.990*, 1748 L 0.996**, 1750 A 1.000**, 1758 T 0.954*, 1759 L 0.997**, 1780 G 0.999** |
| ycf2 | −10,302.30873 |
p0 = 0.96727p = 5.07671q = 3.06985 (p1 = 0.03273)ω = 65.06865 |
847 R 0.994**, 1008 D 1.000**, 1087 G 0.993**, 1353 L 1.000**, 1390 T 0.993**, 1417 E 0.993**, 1421 S 0.994**, 1461 P 0.994**, 1654 H 0.993**, 1677 I 0.993**, 2117 R 0.994**, 1997 T 0.993**, 2117 R 0.994**, 2231 Q 0.994**, 2247 R 1.000**, 2317 L 0.972*, 2319 H 0.993**, 2321 T 0.999**, 2322 G 0.995**, 2323 E 0.993**, 2324 R 0.993**, 2325 F 0.999**, 2327 I 0.993**, 2328 P 0.994** |
| ycf3 | − 735.294401 |
p0 = 0.98001p = 0.00500q = 1.68882 (p1 = 0.01999)ω = 32.38804 |
44 M 0.998** |
The degree of freedom for each gene was 38; * and ** indicate posterior probability higher than 0.95 and 0.99, respectively