7
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Chloroplast DNA variation in a hyperdiverse tropical tree community

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          • We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.

          • We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.

          • Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).

          • Despite large heterogeneities caused by genus‐specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species‐rich tropical forests.

          Related collections

          Most cited references56

          • Record: found
          • Abstract: found
          • Article: not found

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            The Bioperl toolkit: Perl modules for the life sciences.

            The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
              Bookmark
              • Record: found
              • Abstract: not found
              • Book Chapter: not found

              Windows 95/98/NT

                Bookmark

                Author and article information

                Contributors
                remy.petit@inra.fr
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                26 March 2019
                April 2019
                : 9
                : 8 ( doiID: 10.1002/ece3.2019.9.issue-8 )
                : 4897-4905
                Affiliations
                [ 1 ] BIOGECO INRA, Univ. Bordeaux Cestas France
                [ 2 ] INRA UMR 0745 EcoFoG (Ecologie des forêts de Guyane) Kourou France
                [ 3 ] AMAP, IRD, Cirad, CNRS, INRA Université de Montpellier Montpellier France
                [ 4 ] INRA, UR629 Ecologie des Forêts Méditerranéennes URFM Avignon France
                Author notes
                [*] [* ] Correspondence

                Rémy J. Petit, INRA, Cestas, France.

                Email: remy.petit@ 123456inra.fr

                Author information
                https://orcid.org/0000-0001-8853-7133
                https://orcid.org/0000-0002-8951-2680
                https://orcid.org/0000-0002-4809-1453
                Article
                ECE35096
                10.1002/ece3.5096
                6476754
                93a56f7a-aee5-4a98-b294-5b455afcb661
                © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 16 August 2018
                : 11 February 2019
                : 01 March 2019
                Page count
                Figures: 1, Tables: 3, Pages: 9, Words: 7614
                Funding
                Funded by: Agence Nationale de la Recherche
                Award ID: ANR-10-LABX-25-01
                Funded by: Institut National de la Recherche Agronomique
                Award ID: Bibliothèque du vivant
                Award ID: Speed@ID
                Award ID: projet innovant EFPA-INRA
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece35096
                April 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.2.1 mode:remove_FC converted:22.04.2019

                Evolutionary Biology
                chloroplast dna,dna barcoding,genetic diversity,hybridization,incomplete lineage sorting,introgression,species diversity,tropical trees

                Comments

                Comment on this article