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      Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

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          Abstract

          DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers – COI and 16S – and three different sampling methods: (a) homogenized Malaise trap samples (homogenate), (b) preservative ethanol from the same samples, and (c) soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is significantly different from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol while strong and large taxa are overrepresented in homogenate. For soil samples, highly degenerate COI primers pick up large amounts of nontarget DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in molecular operational taxonomic unit (MOTU) content was found between the trap and the soil samples. Our results demonstrate that none of the tested sampling approaches is satisfactory on its own. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.

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          Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

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            Environmental DNA for wildlife biology and biodiversity monitoring.

            Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research. Copyright © 2014 Elsevier Ltd. All rights reserved.
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              obitools: a unix-inspired software package for DNA metabarcoding.

              DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
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                Author and article information

                Contributors
                daniel.marquina@nrm.se
                Journal
                Mol Ecol Resour
                Mol Ecol Resour
                10.1111/(ISSN)1755-0998
                MEN
                Molecular Ecology Resources
                John Wiley and Sons Inc. (Hoboken )
                1755-098X
                1755-0998
                18 September 2019
                November 2019
                : 19
                : 6 ( doiID: 10.1111/men.v19.6 )
                : 1516-1530
                Affiliations
                [ 1 ] Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
                [ 2 ] Department of Zoology Stockholm University Stockholm Sweden
                [ 3 ] Faculty of Agriculture and Forestry University of Helsinki Helsinki Finland
                [ 4 ] Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
                Author notes
                [*] [* ] Correspondence

                Daniel Marquina, Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.

                Email: daniel.marquina@ 123456nrm.se

                Author information
                https://orcid.org/0000-0001-5722-058X
                https://orcid.org/0000-0002-7568-2515
                https://orcid.org/0000-0002-2957-4791
                https://orcid.org/0000-0002-3929-251X
                Article
                MEN13071
                10.1111/1755-0998.13071
                6899807
                31379089
                2230b50c-87eb-4871-b9ed-84bcd34f10f6
                © 2019 John Wiley & Sons Ltd

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 02 April 2019
                : 26 June 2019
                : 03 July 2019
                Page count
                Figures: 6, Tables: 2, Pages: 15, Words: 12096
                Funding
                Funded by: European Union's Horizon 2020 , open-funder-registry 10.13039/100010661;
                Award ID: 642241
                Funded by: Swedish Research Council , open-funder-registry 10.13039/501100004359;
                Award ID: 2014‐05901
                Categories
                Resource Article
                RESOURCE ARTICLES
                Molecular and Statistical Advances
                Custom metadata
                2.0
                November 2019
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.2 mode:remove_FC converted:05.12.2019

                Ecology
                environmental dna,insects,malaise traps,metabarcoding,nondestructive extraction,preservative ethanol

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