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      Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

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          Abstract

          We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development.

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          Approaching a state shift in Earth's biosphere.

          Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale 'tipping point' highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes.
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            Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

            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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              Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

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                Author and article information

                Journal
                Genes (Basel)
                Genes (Basel)
                genes
                Genes
                MDPI
                2073-4425
                29 October 2019
                November 2019
                : 10
                : 11
                : 858
                Affiliations
                [1 ]Department of Biogeography, University of Trier, 54296 Trier, Germany; krehenwinkel@ 123456uni-trier.de
                [2 ]Department of Integrative Biology, University of California, Berkeley, CA-94720, USA; pomerantz_aaron@ 123456berkeley.edu
                [3 ]Marine Biology Laboratory, Woods Hole, MA-02543, USA
                [4 ]LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany
                [5 ]South African National Biodiversity Institute, National Zoological Garden, Pretoria 0002, South Africa
                Author notes
                Author information
                https://orcid.org/0000-0002-6229-3596
                Article
                genes-10-00858
                10.3390/genes10110858
                6895800
                31671909
                6b4a8858-0920-4c0a-a8b2-a07dc6bb2b56
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 17 September 2019
                : 25 October 2019
                Categories
                Review

                portable sequencing,nanopore sequencing,biodiversity monitoring,local capacity building,minion,dna barcoding,long read sequencing

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