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      The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community, Mexico

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          Abstract

          Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as “Endangered” on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species ( Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.

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          Most cited references11

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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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            How to track and assess genotyping errors in population genetics studies.

            Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies.
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              Plant-plant interactions and environmental change.

              R Brooker (2005)
              Natural systems are being subjected to unprecedented rates of change and unique pressures from a combination of anthropogenic environmental change drivers. Plant-plant interactions are an important part of the mechanisms governing the response of plant species and communities to these drivers. For example, competition plays a central role in mediating the impacts of atmospheric nitrogen deposition, increased atmospheric carbon dioxide concentrations, climate change and invasive nonnative species. Other plant-plant interaction processes are also being recognized as important factors in determining the impacts of environmental change, including facilitation and evolutionary processes associated with plant-plant interactions. However, plant-plant interactions are not the only factors determining the response of species and communities to environmental change drivers - their activity must be placed within the context of the wide range of factors that regulate species, communities and ecosystems. A major research challenge is to understand when plant-plant interactions play a key role in regulating the impact of environmental change drivers, and the type of role that plant-plant interactions play. Although this is a considerable challenge, some areas of current research may provide the starting point to achieving these goals, and should be pursued through large-scale, integrated, multisite experiments.
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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, USA )
                1932-6203
                2014
                6 November 2014
                : 9
                : 11
                : e111623
                Affiliations
                [1 ]Forestry and Wood Industry Institute, Universidad Juárez del Estado de Durango, Durango, Mexico
                [2 ]Higher Technical School of Agricultural and Forestry Engineering, Universidad Castilla-La Mancha, Albacete, Spain
                University of Innsbruck, Austria
                Author notes

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

                Conceived and designed the experiments: CW SLSR. Performed the experiments: CW SLSR CZQP. Analyzed the data: SLSR CW CALS. Contributed reagents/materials/analysis tools: SLSR CZQP CW CALS. Wrote the paper: SLSR CW CZQP DMN EHT. Revised the paper: CALS. Helped create the map: CALS.

                Article
                PONE-D-14-25750
                10.1371/journal.pone.0111623
                4222919
                25375134
                547847ea-73a6-4fa6-a4f3-e623107421e0
                Copyright @ 2014

                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 June 2014
                : 2 October 2014
                Page count
                Pages: 11
                Funding
                This study was supported by joint funding from the Mexican Council of Science and Technology (CONACyT: http://www.conacyt.gob.mx/) and the Ministry of Education (SEP: http://www.sep.gob.mx/; Project CB-2010-01 158054). CW received the funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Genetics
                Conservation Genetics
                Ecology
                Ecology and Environmental Sciences
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                The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.

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