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

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

Gene	Model compared	Df^a	-2dlnL^b	p-values of LRT^c	Positively selected sites^d
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)

ISSN: 1471-2229