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      Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

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          Abstract

          DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix ( rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.

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          A DNA barcode for land plants.

          DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
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            Community diversity: relative roles of local and regional processes.

            The species richness (diversity) of local plant and animal assemblages-biological communities-balances regional processes of species formation and geographic dispersal, which add species to communities, against processes of predation, competitive exclusion, adaptation, and stochastic variation, which may promote local extinction. During the past three decades, ecologists have sought to explain differences in local diversity by the influence of the physical environment on local interactions among species, interactions that are generally believed to limit the number of coexisting species. But diversity of the biological community often fails to converge under similar physical conditions, and local diversity bears a demonstrable dependence upon regional diversity. These observations suggest that regional and historical processes, as well as unique events and circumstances, profoundly influence local community structure. Ecologists must broaden their concepts of community processes and incorporate data from systematics, biogeography, and paleontology into analyses of ecological patterns and tests of community theory.
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              Opposing effects of competitive exclusion on the phylogenetic structure of communities.

              Though many processes are involved in determining which species coexist and assemble into communities, competition is among the best studied. One hypothesis about competition's contribution to community assembly is that more closely related species are less likely to coexist. Though empirical evidence for this hypothesis is mixed, it remains a common assumption in certain phylogenetic approaches for inferring the effects of environmental filtering and competitive exclusion. Here, we relate modern coexistence theory to phylogenetic community assembly approaches to refine expectations for how species relatedness influences the outcome of competition. We argue that two types of species differences determine competitive exclusion with opposing effects on relatedness patterns. Importantly, this means that competition can sometimes eliminate more different and less related taxa, even when the traits underlying the relevant species differences are phylogenetically conserved. Our argument leads to a reinterpretation of the assembly processes inferred from community phylogenetic structure.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Writing – review & editing
                Role: VisualizationRole: Writing – review & editing
                Role: Writing – review & editing
                Role: Investigation
                Role: Formal analysis
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                19 October 2017
                2017
                : 12
                : 10
                : e0185861
                Affiliations
                [1 ] Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
                [2 ] Environmental and Life Sciences, Faculty of Science, University of Brunei Darussalam, Gadong, Brunei Darussalam
                [3 ] Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, United Kingdom
                [4 ] School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
                [5 ] School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
                [6 ] Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
                [7 ] Geography, University of Exeter, Exeter, United Kingdom
                [8 ] Sarawak Forest Department, Kuching, Sarawak, Malaysia
                [9 ] School of Biological Science, University of Aberdeen, Aberdeen, United Kingdom
                Chinese Academy of Forestry, CHINA
                Author notes

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

                Author information
                http://orcid.org/0000-0001-8771-9154
                Article
                PONE-D-17-21122
                10.1371/journal.pone.0185861
                5648112
                29049301
                872d723d-f67f-4310-a601-193ba2ba63da
                © 2017 Heckenhauer 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
                : 2 June 2017
                : 20 September 2017
                Page count
                Figures: 7, Tables: 2, Pages: 24
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002428, Austrian Science Fund;
                Award ID: P26548-B22
                Award Recipient :
                This work was funded by the Austrian Science Fund FWF ( https://www.fwf.ac.at). The grant (P26548-B22) was given to R. Samuel. 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
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Ecology
                Community Ecology
                Community Structure
                Ecology and Environmental Sciences
                Ecology
                Community Ecology
                Community Structure
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                DNA barcoding
                Research and analysis methods
                Molecular biology techniques
                DNA barcoding
                Biology and life sciences
                Evolutionary biology
                Evolutionary systematics
                Molecular systematics
                DNA barcoding
                Biology and life sciences
                Taxonomy
                Evolutionary systematics
                Molecular systematics
                DNA barcoding
                Computer and information sciences
                Data management
                Taxonomy
                Evolutionary systematics
                Molecular systematics
                DNA barcoding
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Sequence Databases
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Databases
                Biology and Life Sciences
                Ecology
                Ecosystems
                Forests
                Ecology and Environmental Sciences
                Ecology
                Ecosystems
                Forests
                Ecology and Environmental Sciences
                Terrestrial Environments
                Forests
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Trees
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Flowering Plants
                Custom metadata
                Topographical raw data were provided by the CTFS-ForestGEO network and is therefore restricted. Sequences are uploaded to the Barcode of Life Datasystem under the code DS-PCSBRU1 (BOLD-IDs are provided in S1 Table) and to Genbank (accession numbers are provided in S1 Table). All other relevant data are within the paper and its Supporting Information files ( S1S3 Tables, S1S5 Texts). Additional data Requests may be sent to Dr. Kamariah Abu Salim: Environmental and Life Sciences, Faculty of Science, University of Brunei Darussalam, Gadong, BE1410, Brunei Darussalam. e-mail: udhl_2003@ 123456yahoo.com ; and Dr. Stuart Davies: Director of Centre for Tropical Forest Science, Smithsonian Tropical Research Institute, Washington DC, USA. e-mail: daviess@ 123456si.edu .

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