Dataset Information

Divergent Population Genetic Structure of the Endangered Helianthemum (Cistaceae) and Its Implication to Conservation in Northwestern China.

ABSTRACT: Population genetic studies provide a foundation for conservation planning, especially for endangered species. Three chloroplast SSRs (mtrnSf-trnGr, mtrnL2-trnF, and mtrnL5-trnL3) and the internal transcribed spacer were used to examine the population structure of Helianthemum in northwestern China. A total of 15 populations of the genus were collected. Nine chloroplast haplotypes and two nuclear genotypes were detected. Both the nuclear and chloroplast data showed two lineages in Helianthemum songaricum, respectively, distributed in Yili Valley and western Ordos Plateau. A total of 66.81% (p < 0.001) of the genetic variation was supported by this lineage split. A Mantel test showed a significant correlation between genetic distance and geographical distance (r = 0.937, p < 0.001). Based on genetic analyses, cpSSRs data support strong genetic divergence between regions. We speculate that the climate change during the late Tertiary and early Quaternary isolated H. songaricum into their current distribution, resulting in interruption of gene flow, leading to isolation and genetic divergence between the two regions. Meanwhile, possible selfing would increase genetic drift in small fragmented populations, that might account for the observed genetic divergence in both regions. Given the loss of genetic diversity and genetic divergence in small populations of Helianthemum in northwestern China immediate conservation management steps should be taken on the species.

SUBMITTER: Su Z

PROVIDER: S-EPMC5214710 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Divergent Population Genetic Structure of the Endangered Helianthemum (Cistaceae) and Its Implication to Conservation in Northwestern China.

Su Zhihao Z Richardson Bryce A BA Zhuo Li L Jiang Xiaolong X

Frontiers in plant science 20170105

Population genetic studies provide a foundation for conservation planning, especially for endangered species. Three chloroplast SSRs (mtrnSf-trnGr, mtrnL2-trnF, and mtrnL5-trnL3) and the internal transcribed spacer were used to examine the population structure of Helianthemum in northwestern China. A total of 15 populations of the genus were collected. Nine chloroplast haplotypes and two nuclear genotypes were detected. Both the nuclear and chloroplast data showed two lineag ...[more]

PMID: 28105040

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Project description:A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.

Project description:BackgroundThe evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species.ResultsIn ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity (He) ranging from 0.2371 to 0.2901. Pairwise FST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size (Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period.ConclusionsOur results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy.

Project description:Red sage (Salvia miltiorrhiza) is a widely used medicinal plant for treatment of cardiovascular and cerebrovascular diseases. Because of excessive excavation by huge market demand and habitat loss by human activities, the wild population resources of S. miltiorrhiza have reduced drastically in recent years. Meanwhile, population status of two closely related species S. bowleyana and S. paramiltiorrhiza were in a trend of decreasing due to their potential replacement of S. miltiorrhiza. Particularly, S. paramiltiorrhiza was threatened and endemic to a small region in eastern China. However, to date there has been no conservation genetic research reported for wild S. miltiorrhiza population and its endangered relatives. Assess the wild germplasm diversity for S. miltiorrhiza and its related species would provide fundamental genetic background for cultivation and molecular breeding of this medicinally important species. In the present study, we investigated the genetic diversity, population structure, and intra/inter-specific differentiation of S. miltiorrhiza and above two relatives using 2b-RAD genome-wide genotyping method. By investigating 81 individuals of S. miltiorrhiza, 55 individuals of S. bowleyana and 15 individuals of S. paramiltiorrhiza from 23 locations in China, we obtained 23,928 SNPs in total. A comparatively high genetic diversity was observed in S. miltiorrhiza (π = 0.0788, H e = 0.0783 ± 0.0007). The observed and expected heterozygosity in populations of these three species ranged from 0.0297 to 0.1481 and 0.0251 to 0.831, respectively. Two major lineage groups were detected in the examined S. miltiorrhiza populations. The results indicated that Dabie Mountain as a genetic diversity center of S. miltiorrhiza and possible complex inter-specific genetic exchange/hybridization occurred between S. miltiorrhiza and the two relatives. We suggest that strategic conservation and germplasm preservation should be considered not only for wild populations of S. miltiorrhiza, but also for its related S. bowleyana and S. paramiltiorrhiza.

Dataset Information

Divergent Population Genetic Structure of the Endangered Helianthemum (Cistaceae) and Its Implication to Conservation in Northwestern China.

Publications

Divergent Population Genetic Structure of the Endangered <i>Helianthemum</i> (Cistaceae) and Its Implication to Conservation in Northwestern China.

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