Spatial genetic structure of Lycium ruthenicum in the Qaidam Basin
Chun-Cheng WANG1, Song-Mei MA,,2,*, Dan ZHANG1, Shao-Ming WANG11Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832000, China 2Key Laboratory of Ecological Corps for Oasis City and Mountain Basin System, College of Science, Shihezi University, Shihezi, Xinjiang 832000, China
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 (hT) and within-population genetic diversity (hS) 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. Keywords：Lycium ruthenicum;Qaidam Basin;chloroplast fragments;genetic variation;genetic structure
Table 1 表1 表1柴达木盆地黑果枸杞自然种群的采样信息及遗传信息 Table 1Sampling information and genetic information of natural populations of Lycium ruthenicum in the Qaidam Basin
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 (Hd ± 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
H1-H7表示为本研究鉴定出的7个叶绿体单倍型。 H1-H7 represents the seven chloroplast haplotypes identified in this study.
A, 单倍型网络, 图中圆圈大小与单倍型频率成正比, 节点间的分支长度大致与单倍型的突变数成正比, 相应分支附近附有步长; 龙葵作为外类群。 Fig. 1Geographical distribution and the haplotype network of seven chloroplast haplotypes (H1-H7) of Lycium ruthenicum in the Qaidam Basin. The population codes in this figure are consistent with Table 1. Pie graphs indicate the frequency of each haplotype at these locations.
A, In the median-joining haplotypes network, the sizes of the circles in the network are proportional to the haplotype frequencies. Branch lengths are roughly proportional to the number of mutation steps between haplotypes and nodes. The true number of steps is shown near the corresponding branch sections. Solanum nigrum was used as outgroup.
Table 3 表3 表3柴达木盆地黑果枸杞种群的分子方差分析(AMOVA) Table 3Analysis of molecular variance (AMOVA) of Lycium ruthenicum in the Qaidam Basin
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
FST= 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
FCT= 0.820 43
组内种群间 Among populations within groups
3
6.917
0.145 46
3.67
FSC= 0.204 18
种群内 Within populations
56
28.408
0.566 95
14.29
FST= 0.857 10
总变异 Total
60
135.003
3.967 37
FCT, 组间的遗传变异指数; FSC, 组内种体间的遗传变异指数; FST, 种群间的遗传变异指数。 FCT, variance among groups relative to total variance; FSC, variance among populations within groups; FST, variance among populations.
Fig. 2Plots of the first three coordinates of the principal coordinates analysis (PCoA) at the population level for Lycium ruthenicum in the Qaidam Basin.
A, 最大似然(ML)树, 分支点上方的数字为大于等于80的自展支持率。B, 贝叶斯树, 分支节点右侧的数字表示所有大于0.80的后验概率值。两系统发育树右侧的黑条表示相应的分支。 Fig. 3Phylogenetic trees of chloroplast haplotypes of Lycium ruthenicum in the Qaidam Basin.
A, Maximum likelihood (ML) tree. Bootstrap values equal to or greater than 80 are shown above the corresponding branching points. B, Bayesian tree. The values on the right of the branching points represent the posterior probability greater than 0.80. The black bars on the right of the two phylogenetic trees indicate the corresponding clades.
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Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species 1 2009
Genetic diversity of the endangered and medically important Lycium ruthenicum Murr. revealed by sequence-related amplified polymorphism (SRAP) markers 2 2012
Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III 2 2007
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,2,*, 张丹1, 王绍明1
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