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      Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

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          Abstract

          Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

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          ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE

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            unmarked: AnRPackage for Fitting Hierarchical Models of Wildlife Occurrence and Abundance

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              Is Open Access

              ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

              Background During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates. Results Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and most of them appeared to introduce taxonomic biases during PCR. Some primers, e.g. ITS1-F, ITS1 and ITS5, were biased towards amplification of basidiomycetes, whereas others, e.g. ITS2, ITS3 and ITS4, were biased towards ascomycetes. The assumed basidiomycete-specific primer ITS4-B only amplified a minor proportion of basidiomycete ITS sequences, even under relaxed PCR conditions. Due to systematic length differences in the ITS2 region as well as the entire ITS, we found that ascomycetes will more easily amplify than basidiomycetes using these regions as targets. This bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi. Conclusions We conclude that ITS primers have to be selected carefully, especially when used for high-throughput sequencing of environmental samples. We suggest that different primer combinations or different parts of the ITS region should be analyzed in parallel, or that alternative ITS primers should be searched for.
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                Author and article information

                Journal
                Molecular Ecology
                Mol Ecol
                Wiley
                09621083
                February 2016
                February 2016
                January 18 2016
                : 25
                : 4
                : 929-942
                Affiliations
                [1 ]SPYGEN; Savoie Technolac-Bât. Koala 17, Rue du Lac Saint-André-BP 274 Le Bourget-du-Lac Cedex 73375 France
                [2 ]Laboratoire d'Ecologie Alpine (LECA); CNRS; Grenoble 38000 France
                [3 ]Laboratoire d'Ecologie Alpine (LECA); Univ. Grenoble Alpes; Grenoble 38000 France
                [4 ]Laboratoire Biogéographie et Ecologie des Vertébrés; CEFE UMR 5175; Montpellier 34293 France
                [5 ]Hydrosystems and Bioprocesses Research Unit; IRSTEA; Antony Cedex 92761 France
                [6 ]RAVON; Postbus 1413 Nijmegen 6501 BK The Netherlands
                [7 ]Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade Copenhagen Denmark
                [8 ]Direction de l'Action Scientifique et Technique; ONEMA; Vincennes 94300 France
                [9 ]Rhône-Alpes Regional Direction; ONEMA; Bron 69500 France
                [10 ]Centre for Environment, Fisheries and Aquaculture Science; Pakefield Road Lowestoft Suffolk NR33 0HT UK
                [11 ]Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON K9J 7B8 Canada
                [12 ]Pole ONEMA/IRSTEA Hydroécologie des plans d'eau; Centre d'Aix-en-Provence; IRSTEA UR HYAX; Aix-en-Provence 13182 France
                [13 ]Le Sambuc; Tour du Valat; Arles 13200 France
                [14 ]Agence Centre-Ouest; Ecosphère; Orléans 45000 France
                [15 ]LNHE Department; EDF R&D; Chatou Cedex 78401 France
                [16 ]Natural History Museum of Denmark; University of Copenhagen; Universitetsparken 15 Copenhagen 2100 Denmark
                Article
                10.1111/mec.13428
                26479867
                c5db5fa4-1844-464c-8663-8136cb2f38c2
                © 2016

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

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