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      Yalongjiang River Has Had an Important Role in the Dispersal and Divergence of Rosa soulieana in the Hengduan Mountains of China

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          Abstract

          The Hengduan Mountains are the core of the Sino-Himalayan Floristic Region. Rosa soulieana Crép. is an important wild rose species that is widely distributed in the Hengduan Mountains. To provide better future utilization of this wild rose, and also to add some possible proof of the effect of geomorphological and ecological characteristics of the Hengduan Mountains on the current spatial distribution and genetic diversity of local species, the genetic diversity and genetic structure of 556 individuals from 37 populations of R. soulieana were studied using fluorescent amplified fragment length polymorphisms (AFLPs). R. soulieana showed a moderately high level of genetic diversity and a high level of genetic differentiation at the species level. The total percentage of polymorphic loci, total heterozygosity ( Ht), Shannon index ( I), and heterozygosity value within populations ( Hs) were 97.8%, 0.253, 0.339, and 0.139, respectively. More than half of the total genetic variation (54.0%) occurred within populations, and the overall gene differentiation coefficient ( Gst) was 0.451. The genetic differentiation among populations was positively and significantly correlated with geographic distance. The neighbor-joining cluster and the Bayesian analysis divided all the populations and individuals into 3 groups, and did not support the morphology based intraspecific varieties. The results confirmed that the ancient R. soulieana of the third group survived in northwestern Yunnan and Yalongjiang valley and then moved upnorth along the valley. The spatial distribution of the other two groups was the result of allopatric divergence due to long period of adaptation to the different climatic conditions of its distribution at either side of the Yalongjiang River.

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          Estimation of average heterozygosity and genetic distance from a small number of individuals.

          M Nei (1978)
          The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.
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            AFLP: a new technique for DNA fingerprinting.

            A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50-100 restriction fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity.
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              Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants.

              A compilation was made of 307 studies using nuclear DNA markers for evaluating among- and within-population diversity in wild angiosperms and gymnosperms. Estimates derived by the dominantly inherited markers (RAPD, AFLP, ISSR) are very similar and may be directly comparable. STMS analysis yields almost three times higher values for within-population diversity whereas among-population diversity estimates are similar to those derived by the dominantly inherited markers. Number of sampled plants per population and number of scored microsatellite DNA alleles are correlated with some of the population genetics parameters. In addition, maximum geographical distance between sampled populations has a strong positive effect on among-population diversity. As previously verified with allozyme data, RAPD- and STMS-based analyses show that long-lived, outcrossing, late successional taxa retain most of their genetic variability within populations. By contrast, annual, selfing and/or early successional taxa allocate most of the genetic variability among populations. Estimates for among- and within-population diversity, respectively, were negatively correlated. The only major discrepancy between allozymes and STMS on the one hand, and RAPD on the other hand, concerns geographical range; within-population diversity was strongly affected when the former methods were used but not so in the RAPD-based studies. Direct comparisons between the different methods, when applied to the same plant material, indicate large similarities between the dominant markers and somewhat lower similarity with the STMS-based data, presumably due to insufficient number of analysed microsatellite DNA loci in many studies.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                29 June 2016
                2016
                : 11
                : 6
                : e0158586
                Affiliations
                [1 ]Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
                [2 ]National Engineering Research Center for Ornamental Horticulture / Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
                [3 ]Life Science Department, Yunnan Normal University, Kunming, China
                University of Gottingen, GERMANY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: HS. Performed the experiments: HYJ YHZ. Analyzed the data: YHZ QGW. Contributed reagents/materials/analysis tools: XQQ HJY HZ. Wrote the paper: HYJ.

                Article
                PONE-D-15-46745
                10.1371/journal.pone.0158586
                4927166
                27355209
                a1faaac0-0fae-4f92-9d37-60ec2dc1652b
                © 2016 Jian et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 11 November 2015
                : 17 June 2016
                Page count
                Figures: 7, Tables: 4, Pages: 20
                Funding
                Funded by: Major Program of National Natural Science Foundation of China
                Award ID: 31590820
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31260198
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31460050
                Award Recipient :
                Funded by: Academic and Technical Talents Training Project of Yunnan Province
                Award ID: 2013 HB092
                Award Recipient :
                This study was supported by Major Program of National Natural Science Foundation of China (31590820 to HS), Major Program of National Natural Science Foundation of China (31590823 to HS), National Natural Science Foundation of China (31260198 to HYJ), National Natural Science Foundation of China (31460050 Dr. Yonghong Zhang), Academic and Technical Talents Training Project of Yunnan Province (2013 HB092 to HYJ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
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                Earth Sciences
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                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
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                Earth Sciences
                Geomorphology
                Topography
                Landforms
                Mountains
                Ecology and Environmental Sciences
                Terrestrial Environments
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                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Amplified Fragment Length Polymorphism
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Amplified Fragment Length Polymorphism
                Biology and Life Sciences
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                Ecology
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