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      Coral reef ecosystem functioning: eight core processes and the role of biodiversity

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          A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

          Introduction The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile (“universal”) COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results We first design a new PCR primer within the highly variable mitochondrial COI region, the “mlCOIintF” primer. We then show that this newly designed forward primer combined with the “jgHCO2198” reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.
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            Evaluating life-history strategies of reef corals from species traits.

            Classifying the biological traits of organisms can test conceptual frameworks of life-history strategies and allow for predictions of how different species may respond to environmental disturbances. We apply a trait-based classification approach to a complex and threatened group of species, scleractinian corals. Using hierarchical clustering and random forests analyses, we identify up to four life-history strategies that appear globally consistent across 143 species of reef corals: competitive, weedy, stress-tolerant and generalist taxa, which are primarily separated by colony morphology, growth rate and reproductive mode. Documented shifts towards stress-tolerant, generalist and weedy species in coral reef communities are consistent with the expected responses of these life-history strategies. Our quantitative trait-based approach to classifying life-history strategies is objective, applicable to any taxa and a powerful tool that can be used to evaluate theories of community ecology and predict the impact of environmental and anthropogenic stressors on species assemblages. © 2012 Blackwell Publishing Ltd/CNRS.
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              Trophic Structure and Productivity of a Windward Coral Reef Community on Eniwetok Atoll

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                Author and article information

                Journal
                Frontiers in Ecology and the Environment
                Front Ecol Environ
                Wiley
                1540-9295
                1540-9309
                July 30 2019
                July 30 2019
                Affiliations
                [1 ]Tennenbaum Marine Observatories Network and Smithsonian Environmental Research CenterSmithsonian Institution Edgewater MD
                [2 ]Department of Biological SciencesSimon Fraser University Burnaby Canada
                [3 ]Bigelow Laboratory for Ocean Sciences East Boothbay ME
                [4 ]Department of Invertebrate ZoologyNational Museum of Natural HistorySmithsonian Institution Washington DC
                [5 ]PSL Université Paris: EPHE‐UPVD‐CNRSUSR 3278 CRIOBEUniversité de Perpignan Perpignan France
                [6 ]Laboratoire d'Excellence “CORAIL” Perpignan France
                [7 ]Department of Ecology and Evolutionary BiologyUniversity of Toronto Toronto Canada
                [8 ]Marine ProgramWildlife Conservation Society New York NY
                Article
                10.1002/fee.2088
                b125dad1-9c9a-435f-b282-99ae66db0978
                © 2019

                http://doi.wiley.com/10.1002/tdm_license_1.1

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