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Table 4 Likelihood ratio tests to identify positively selected sites within the accD and ycf1 genes across 21 Alpinia plastomes

From: Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

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  
  1. aDegree of freedom
  2. bDifference between the log likelihood values
  3. cLRT Likelihood Ratio Test
  4. dSites potentially under positive selection, indicated by the high Empirical Bayes values (‘*’: > 0.95; ‘**’: > 0.99)