Genetic diversity of Herpetospermum caudigerum (Ser.) Baill using AFLP and chloroplast microsatellites

Figures & data

Table 1. Location and sample size of the four populations in the study.

Altitude (m)	Sample size	Location	Longitude	Latitude
2800	18	Bomi, Tibet Plateau	95° 36′18.69″E	30° 03′17.19″N
3000	16	Nanyiluozha, Tibet Plateau	94° 12′02.98″E	29° 10′01.74″N
3100	18	Bomi, Tibet Plateau	96° 05′28.06″E	29° 45′40.06″N
3300	18	Bomi, Tibet Plateau	96° 06′09.89″E	29° 52′41.43″N

Table 2. Ten primer combinations used for genetic analysis of the four H. caudigerum Baill populations.

Primer pair	Number of total bands	Number of polymorphic bands	Polymorphic rates (%)	Na	Ne	H	I	Ht	Hs	Gst	Nm
E14 + M12	43	31	72	1.390	1.198	0.119	0.182	0.153	0.119	0.223	1.744
E33 + M13	32	20	63	1.422	1.209	0.123	0.187	0.154	0.123	0.201	1.993
E21 + M21	28	16	57	1.420	1.229	0.136	0.205	0.155	0.136	0.121	3.642
E42 + M32	39	26	67	1.391	1.194	0.119	0.183	0.164	0.119	0.276	1.315
E34 + M23	41	27	66	1.384	1.228	0.132	0.196	0.151	0.132	0.129	3.364
E43 + M44	48	28	58	1.318	1.179	0.105	0.157	0.159	0.105	0.342	0.962
E22 + M33	57	22	39	1.193	1.095	0.057	0.088	0.089	0.057	0.359	0.892
E33 + M34	38	20	53	1.230	1.136	0.080	0.120	0.161	0.080	0.502	0.496
E41 + M43	48	37	77	1.448	1.238	0.139	0.209	0.221	0.139	0.373	0.840
E44 + M43	52	29	56	1.327	1.170	0.100	0.152	0.154	0.100	0.349	0.933
Mean	42.6	25.6	60.7	1.352	1.188	0.111	0.168	0.156	0.111	0.287	1.618

Table 3. Analysis of molecular variance for four high altitude populations of H. caudigerum Baill based on AFLP and cpDNA sequence data.

	Source of variation	df	SSD	% variation
AFLP	Among populations	23	1248.526	63.72
	Within populations	168	605.875	36.28
	Total	191	1854.401
cpSSR	Among populations	3	364.676	96.79
	Within populations	66	15.167	3.21
	Total	69	379.843

Table 4. Mantel test relationship between geographic (above diagonal) and genetic distance (below diagonal).

	2800 m	3000 m	3100 m	3300 m
2800 m	1	168.03	57.160	51.853
3000 m	0.096	1	194.771	200.502
3100 m	0.074	0.017	1	13.081
3300 m	0.075	0.085	0.086	1

Figure 1. UPGMA dendrogram of 70 accessions using AFLP.

Note: Samples from 2800 m (up-pointing triangles); samples from 3000 m (down-pointing triangles); samples from 3100 m (filled circles); samples from 3300 m (open circles).

Figure 2. Individual-based cluster analysis using STRUCTURE for K = 4 based on AFLP data (a) and cpDNA data (b).

Note: samples from 2800 m (blue); samples from 3000 m (yellow); samples from 3100 m (green); samples from 3300 m (red).

Table 5. Genetic diversity information of cpDNA sequences in H. caudigerum Baill populations from different altitudes.

cpDNA fragments	Length (bp)	h	Vs	Ps	Is	k	Pi	Hd	Vh	Sh	Tajima’s D test
trnL-trnF-300	300	5	20	20	82	7.871	0.036	0.720	0.00052	0.023	2.71990 (P < 0.01)
trnL-trnF-396	396	3	8	8	20	3.179	0.008	0.518	0.00259	0.051	2.34963 (P < 0.05)
combined	696	7	28	28	102	11.050	0.019	0.748	0.00057	0.024	2.84515 (P < 0.01)

Table 6. Haplotype distribution based on cpDNA sequences in different altitude populations of H. caudigerum Baill.

Altitudes (m)	Haplotype frequency (n)
	H1	H2	H3	H4	H5	H6	H7
2800	1.000 (18)
3000		0.667 (16)
3100			1.000 (2)	1.000 (4)	0.579 (11) (11) (11)	0.500 (1)
3300		0.333 (8)			0.421 (8)	0.500 (1)	1.000 (1)
Overall	0.257	0.343	0.029	0.057	0.271	0.029	0.014

Table 7. Fst value pairwise difference of populations of H. caudigerum Baill.

	2800 m	3000 m	3100 m	3300 m
2800 m	0.00000
3000 m	1.00000	0.00000
3100 m	0.97678	0.48949	0.00000
3300 m	0.99047	0.39470	0.17412	0.00000

Figure 3. cpDNA haplotype network based on cpDNA data.

Note: samples from 2800 m (blue); samples from 3000 m (yellow); samples from 3100 m (green); samples from 3300 m (red).

Data archiving statement

There are no linked research data sets for this submission. The following reason is given: All data generated or analyzed during this study are included in this published article and its Additional files.