Spatial genetic structure of Lycium ruthenicum in the Qaidam Basin

doi:10.17521/cjpe.2019.0298

Abstract

Abstract:

Aims Based on the cpDNA sequences, we studied the genetic diversity, genetic structure and haplotype evolution of wild Lycium ruthenicum in the Qaidam Basin and provided the scientific basis for the genetic conservation of this species.
Methods We used three filtered high polymorphic cpDNA fragments (psbA-trnH, psbK-psbI and trnV) to study the genetic variation pattern of L. ruthenicum in the Qaidam Basin by employing the population genetic analysis methods. The molecular diversity indices were calculated by using the software of DnaSP 6.0 and Permut 2.0. Genetic differentiation among populations and the defined groups was estimated by the AMOVA analysis. The median-joining network and principal coordinate analysis (PCoA) were used to identify the clustering relationship of haplotype. The maximum likelihood method and Bayesian method were used to reconstruct the phylogenetic tree based on cpDNA haplotypes.
Important findings The combined length of psbA-trnH, psbK-psbI and trnV was 1 454 bp. 14 polymorphic sites were detected, and a total of seven haplotypes were identified. The total genetic diversity (h_T) and within-population genetic diversity (h_S) were 0.916 and 0.512, respectively. Results from AMOVA suggested that more than 80% of the observed variation was due to differences among groups and populations. The maximum likelihood analysis and Beast analysis revealed that seven haplotypes clustered into two clusters, corresponding to Golmud and Delingha regions and Nuomuhong region, respectively. The revealed topological structure and clusters of haplotype network and PCoA analyses were consistent with the phylogenetic trees. Results of the Mantel test (r = 0.591 1, p = 0.000 9) indicated a non-significant correlation between geographical distance and genetic distance. The L. ruthenicum populations in the Qaidam Basin have high levels of genetic diversity and significant genetic differentiation among populations. In relation to conservation management, we identified the Nuomuhong forestry station and Xinle Village of Golmud City as having a high degree of genetic diversity and these should be the areas of the greatest focus for conservation.

Key words: Lycium ruthenicum, Qaidam Basin, chloroplast fragments, genetic variation, genetic structure

WANG Chun-Cheng, MA Song-Mei, ZHANG Dan, WANG Shao-Ming. Spatial genetic structure of Lycium ruthenicum in the Qaidam Basin[J]. Chin J Plant Ecol, 2020, 44(6): 661-668.

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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2019.0298

https://www.plant-ecology.com/EN/Y2020/V44/I6/661

Figures/Tables 6

References 30

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种群名称及编码 Population name and code	海拔 Altitude (m)	经纬度 Latitude and Longitude	采样数 Sample size	单倍型及个体数 Haplotype and the individual numbers	单倍型多样性 Haplotype diversity (H_d ± SD)	核苷酸多样性 Nucleotide diversity (π ± SD)
德令哈市红光村 Hongguang Village of Delingha City (DLH)	2 970	37.38° N, 97.34° E	10	H1 (2), H4 (8)	0.356 ± 0.025	0.000 73 ± 0.33
都兰县诺木洪林业站 Nuomuhong Forestry Station of Dulan County (NMH1)	2 820	36.41° N, 96.45° E	15	H5 (7), H6 (6), H7 (2)	0.604 ± 0.069	0.000 46 ± 0.09
都兰县诺木洪乡田格力村 Tiangeli Village of Nuomuhong Township of Dulan County (NMH2)	2 762	36.39° N, 96.19° E	12	H5 (5), H7 (7)	0.530 ± 0.053	0.000 37 ± 0.05
格尔木市新乐村 Xinle Village of Golmud City (GEM1)	2 787	36.39° N, 94.86° E	12	H1 (7), H2 (4), H3 (1)	0.591 ± 0.011	0.001 26 ± 0.03
格尔木市大格勒乡 Dagele Township of Golmud City (GEM2)	2 837	36.44° N, 95.75° E	11	H1 (3), H2 (8)	0.436 ± 0.018	0.000 09 ± 0.03

种群名称及编码 Population name and code	海拔 Altitude (m)	经纬度 Latitude and Longitude	采样数 Sample size	单倍型及个体数 Haplotype and the individual numbers	单倍型多样性 Haplotype diversity (H_d ± SD)	核苷酸多样性 Nucleotide diversity (π ± SD)
德令哈市红光村 Hongguang Village of Delingha City (DLH)	2 970	37.38° N, 97.34° E	10	H1 (2), H4 (8)	0.356 ± 0.025	0.000 73 ± 0.33
都兰县诺木洪林业站 Nuomuhong Forestry Station of Dulan County (NMH1)	2 820	36.41° N, 96.45° E	15	H5 (7), H6 (6), H7 (2)	0.604 ± 0.069	0.000 46 ± 0.09
都兰县诺木洪乡田格力村 Tiangeli Village of Nuomuhong Township of Dulan County (NMH2)	2 762	36.39° N, 96.19° E	12	H5 (5), H7 (7)	0.530 ± 0.053	0.000 37 ± 0.05
格尔木市新乐村 Xinle Village of Golmud City (GEM1)	2 787	36.39° N, 94.86° E	12	H1 (7), H2 (4), H3 (1)	0.591 ± 0.011	0.001 26 ± 0.03
格尔木市大格勒乡 Dagele Township of Golmud City (GEM2)	2 837	36.44° N, 95.75° E	11	H1 (3), H2 (8)	0.436 ± 0.018	0.000 09 ± 0.03

单倍型 Haplotype	变异位点 Variable nucleotide sites
	psbA-trnH										psbK-psbI		trnV
	1	10	217	318	319	333	365	371	421	426	528	595	1039	1208
H1	A	C	C	G	G	T	-	G	G	G	-	T	T	G
H2	●	●	●	●	●	●	-	●	●	C	A	●	C	●
H3	●	-	A	●	●	●	-	●	●	●	-	●	C	●
H4	●	●	●	●	●	A	C	●	A	●	-	●	●	●
H5	-	●	●	C	C	●	-	C	A	●	A	C	●	●
H6	-	●	●	C	C	●	-	C	A	●	A	C	●	T
H7	-	●	●	C	C	●	-	C	A	●	A	C	C	●

单倍型 Haplotype	变异位点 Variable nucleotide sites
	psbA-trnH										psbK-psbI		trnV
	1	10	217	318	319	333	365	371	421	426	528	595	1039	1208
H1	A	C	C	G	G	T	-	G	G	G	-	T	T	G
H2	●	●	●	●	●	●	-	●	●	C	A	●	C	●
H3	●	-	A	●	●	●	-	●	●	●	-	●	C	●
H4	●	●	●	●	●	A	C	●	A	●	-	●	●	●
H5	-	●	●	C	C	●	-	C	A	●	A	C	●	●
H6	-	●	●	C	C	●	-	C	A	●	A	C	●	T
H7	-	●	●	C	C	●	-	C	A	●	A	C	C	●

变异来源 Source of variation	自由度 df	平方和 Sum of squares	变异组成 Variance components	变异所占比例 Percentage of variation (%)	固定指数 Fixation index
种群间 Among populations	4	105.305	2.159 37	80.01	F_ST = 0.800 07
种群内 Within populations	55	29.679	0.539 61	19.99
总变异 Total	59	135.953	2.698 99
组间 Among groups	1	100.383	3.254 96	82.04	F_CT = 0.820 43
组内种群间 Among populations within groups	3	6.917	0.145 46	3.67	F_SC = 0.204 18
种群内 Within populations	56	28.408	0.566 95	14.29	F_ST = 0.857 10
总变异 Total	60	135.003	3.967 37