. 2020 Feb 13;15(2):e0229181. doi: 10.1371/journal.pone.0229181

Table 3. Analysis of the variability in different fragments and combination of fragments.

	No. sites	No. variable sites	No. parsimony information sites	No. mutations	No. InDels	Intraspecific distance		Interspecific distance		Nucleotide diversity (Pi)
	No. sites	No. variable sites	No. parsimony information sites	No. mutations	No. InDels	Range	Mean (± SE)	Range	Mean (± SE)	Nucleotide diversity (Pi)
Genome	154,404	2,667	2,436	2,449	4,273	0–0.0021	0.0005±0.0001	0.0007–0.0078	0.0037±0.0001	0.00337
HKLI	3,890	180	132	170	44	0–0.0052	0.0012±0.0002	0.0008–0.0191	0.0082±0.0006	0.00784
HKL	3,255	76	74	71	19	0–0.0034	0.0006±0.0002	0.0003–0.0117	0.0051±0.0001	0.00466
ITS2	239	52	22	55	9	0–0.0807	0.0094±0.0027	0–0.1211	0.0326±0.0013	0.03304
ITS	635	104	58	99	25	0–0.0338	0.0044±0.0011	0–0.0709	0.0235±0.0008	0.02560
trnH-psbA	253	17	17	16	19	0–0.0043	0.0010±0.0003	0–0.0598	0.0147±0.0009	0.01288
matK	1539	37	37	37	0	0–0.0039	0.0007±0.0002	0.0006–0.0123	0.0059±0.0001	0.00537
rbcL	1464	21	19	21	0	0–0.0027	0.0005±0.0001	0–0.0075	0.0033±0.0001	0.00295
ndhF-trnL-UAG	1,381	60	57	52	77	0–0.0052	0.0008±0.0002	0–0.0321	0.0112±0.0011	0.00994
psbM-psdD	3608	163	150	130	582	0–0.0058	0.0014±0.0003	0.0020–0.0202	0.0101±0.0002	0.00907
rps4-trnL-UAA	1,323	56	53	49	138	0–0.0061	0.0016±0.0003	0–0.0238	0.0098±0.0003	0.00892
ycf1	5,565	214	203	223	63	0–0.0044	0.0010±0.0002	0.0016–0.0240	0.0092±0.0003	0.00836
petB-intron	855	30	29	28	17	0–0.0050	0.0012±0.0002	0–0.0200	0.0078±0.0002	0.00703
ndhD	1,509	39	36	41	6	0–0.0020	0.0006±0.0001	0–0.0160	0.0056±0.0002	0.00502

HKL and HKLI represent a combination of three fragments of the plastid genome and a combination of four fragments of universal barcodes, respectively (H: trnH-psbA; K: matK; L: rbcL; I: ITS)