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      Population genetic structure is shaped by historical, geographic, and environmental factors in the leguminous shrub Caragana microphylla on the Inner Mongolia Plateau of China

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          Abstract

          Background

          Understanding how landscape factors, including suites of geographic and environmental variables, and both historical and contemporary ecological and evolutionary processes shape the distribution of genetic diversity is a primary goal of landscape and conservation genetics and may be particularly consequential for species involved in ecological restoration. In this study, we examine the factors that shape the distribution of genetic variation in a leguminous shrub ( Caragana microphylla) important for restoration efforts on the Mongolian Plateau in China. This region houses several major bioclimatic gradients, and C. microphylla is an important restoration species because it stabilizes soils and prevents advancing desertification on the Inner Mongolia Plateau caused by ongoing climate change.

          Results

          We assembled an expansive genomic dataset, consisting of 22 microsatellite loci, four cpDNA regions, and 5788 genome-wide SNPs from ten populations of C. microphylla. We then applied ecological niche modelling and linear and non-linear regression techniques to investigate the historical and contemporary forces that explain patterns of genetic diversity and population structure in C. microphylla on the Inner Mongolia Plateau. We found strong evidence that both geographic and environmental heterogeneity contribute to genetic differentiation and that the spatial distribution of genetic diversity in C. microphylla appears to result partly from the presence of a glacial refugium at the southwestern edge of its current range.

          Conclusions

          These results suggest that geographic, environmental, and historical factors have all contributed to spatial genetic variation in this ecologically important species. These results should guide restoration plans to sustain genetic diversity during plant translocations.

          Electronic supplementary material

          The online version of this article (10.1186/s12870-017-1147-7) contains supplementary material, which is available to authorized users.

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          Most cited references31

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          Universal primers for amplification of three non-coding regions of chloroplast DNA.

          Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
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            Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation.

            Local adaptation is a central feature of most species occupying spatially heterogeneous environments, and may factor critically in responses to environmental change. However, most efforts to model the response of species to climate change ignore intraspecific variation due to local adaptation. Here, we present a new perspective on spatial modelling of organism-environment relationships that combines genomic data and community-level modelling to develop scenarios regarding the geographic distribution of genomic variation in response to environmental change. Rather than modelling species within communities, we use these techniques to model large numbers of loci across genomes. Using balsam poplar (Populus balsamifera) as a case study, we demonstrate how our framework can accommodate nonlinear responses of loci to environmental gradients. We identify a threshold response to temperature in the circadian clock gene GIGANTEA-5 (GI5), suggesting that this gene has experienced strong local adaptation to temperature. We also demonstrate how these methods can map ecological adaptation from genomic data, including the identification of predicted differences in the genetic composition of populations under current and future climates. Community-level modelling of genomic variation represents an important advance in landscape genomics and spatial modelling of biodiversity that moves beyond species-level assessments of climate change vulnerability.
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              The 'abundant centre' distribution: to what extent is it a biogeographical rule?

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                Author and article information

                Contributors
                22953491@qq.com
                991180581@qq.com
                xueminwang1@sohu.com
                273685441@qq.com
                ianwang@berkeley.edu
                wangzan@caas.cn
                Journal
                BMC Plant Biol
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central (London )
                1471-2229
                13 November 2017
                13 November 2017
                2017
                : 17
                : 200
                Affiliations
                [1 ]GRID grid.464332.4, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, ; Beijing, 100193 China
                [2 ]ISNI 0000 0000 9888 756X, GRID grid.464353.3, Animal Science and Technology College, , Jilin Agricultural University, ; Changchun, 130118 China
                [3 ]ISNI 0000 0001 2181 7878, GRID grid.47840.3f, Department of Environmental Science, Policy, and Management, , University of California, ; Berkeley, CA 94720 USA
                Article
                1147
                10.1186/s12870-017-1147-7
                5683519
                29132298
                de2f897d-d5da-4a77-b6ac-f72714209feb
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 15 March 2017
                : 31 October 2017
                Funding
                Funded by: the Agricultural Science and Technology Innovation Program of China
                Award ID: ASTIP-IAS10
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Plant science & Botany
                ecological niche,isolation by distance,isolation by environment,plant ecology,population genetic structure,restoration ecology

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