Table 4.
Likelihood ratio tests to identify positively selected sites within the accD and ycf1 genes across 21 Alpinia plastomes
| Gene | Model compared | Dfa | -2dlnLb | p-values of LRTc | Positively selected sitesd |
|---|---|---|---|---|---|
| accD | M1a (neutral) vs. M2a (selection) | 2 | 17.060598 | 0.000197396 | |
| M7 (beta) vs. M8 (beta & ω >1) | 2 | 17.143904 | 0.000189343 |
1 F 0.995**, 24 I 0.997**, 181 N 0.977* |
|
| M8a (ω=1) vs. M8 (selection) | 1 | 17.051707 | 0.000036376 | ||
| ycf1 | M1a (neutral) vs. M2a (selection) | 2 | 17.751095 | 0.000139765 | |
| M7 (beta) vs. M8 (beta & ω >1) | 2 | 15.933493 | 0.000346805 |
3 F 0.964*, 141 F 0.969*, 259 E 0.968*, 303 Y 0.965*, 326 L 0.990** |
|
| M8a (ω=1) vs. M8 (selection) | 1 | 15.839639 | 0.000068943 |
aDegree of freedom
bDifference between the log likelihood values
cLRT Likelihood Ratio Test
dSites potentially under positive selection, indicated by the high Empirical Bayes values (‘*’: > 0.95; ‘**’: > 0.99)