Table 7.

Positive selection sites identified in the chloroplast genomes of four Bulbophyllum species.

Gene	Model	Ln L	LRT P-value	Positive sites
ndhF	M0	−3367.871835	M0 vs. M3: 4.99 × 10−3 M1a vs. M2a: 1.57 × 10−1 M7 vs. M8: 8.57 × 10−2	588 E 0.976∗
	M3	−3360.438925
	M1a	−3362.318789
	M2a	−3360.405802
	M7	−3363.243214
	M8	−3360.786314
ndhK	M0	−1047.915524	M0 vs. M3: 2.00 × 10−8 M1a vs. M2a: 1.16 × 10−6 M7 vs. M8: 9.87 × 10−7	214 P 0.961∗, 216 G 0.954∗, 217 Q 0.971∗, 218 Y 0.993∗∗, 219 L 0.996∗∗, 220 P 0.995∗∗
	M3	−1027.108483
	M1a	−1040.774810
	M2a	−1027.108483
	M7	−1041.140233
	M8	−1027.311588
ycf2	M0	−9561.901080	M0 vs. M3: 1.87 × 10−5 M1a vs. M2a: 2.12 × 10−5 M7 vs. M8: 1.15 × 10−5	563 G 0.973∗, 564 C 0.981∗, 774 L 0.951∗, 919 I 0.951∗
	M3	−9548.340210
	M1a	−9559.101790
	M2a	−9548.340212
	M7	−9559.710001
	M8	−9548.339220
rbcL	M0	−2128.95659	M0 vs. M3: 4.01 × 10−5 M1a vs. M2a: 5.33 × 10−4 M7 vs. M8: 7.95 × 10−5	96 A 0.952∗, 98 V 0.964∗, 101 E 0.975∗
	M3	−2125.041535
	M1a	−2150.834797
	M2a	−2143.297217
	M7	−2152.737025
	M8	−2143.297216
rps4	M0	−917.908875	M0 vs. M3: 3.01 × 10−3 M1a vs. M2a: 3.33 × 10−3 M7 vs. M8: 1.04 × 10−3	183 L 0.998∗∗
	M3	−909.907038
	M1a	−915.613890
	M2a	−909.909196
	M7	−916.783516
	M8	−909.913519
rps16	M0	−366.198755	M0 vs. M3: 4.00 × 10−9 M1a vs. M2a: 0.00 M7 vs. M8: 0.00	21 K 0.986∗
	M3	−343.729536
	M1a	−368.201071
	M2a	−343.729536
	M7	−370.023492
	M8	−343.729564

∗P < 0.05, ∗∗P < 0.001.