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      Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation: lessons from the UK diatom metabarcoding exercise

      Metabarcoding and Metagenomics

      Pensoft Publishers

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          Abstract

          Development of effective metabarcoding-based tools for ecological assessment requires more than just detailed knowledge of ecology and molecular genetics. There is also a need to understand the context within which they will be used, and for the organisation that uses it to understand the techniques involved and, more especially, how the data that are produced differs from that generated by traditional ecological methods. Lessons learnt during the development of a metabarcoding tool for phytobenthos in the UK are set out in this paper. This attempted to develop a molecular “mirror” of the existing light microscopy-based approach to ecological assessment. Although this conservative approach does not exploit the full potential of metabarcoding data, it does mean that benchmarks exist against which performance and data can be judged. However, the pace of developments within molecular ecology means that regulators will need to find ways of incorporating new scientific insights whilst, at the same time, ensuring a stable regulatory regime. Installation of a metabarcoding technique within a regulatory organisation, in other words, is more than a transaction in which one approach is switched for another. A deeper transformation of the organisation is required.

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          Most cited references 24

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          Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing.

          Biological monitoring has failed to develop from simple binary assessment outcomes of the impacted/unimpacted type, towards more diagnostic frameworks, despite significant scientific effort over the past fifty years. It is our assertion that this is largely because of the limited information content of biological samples processed by traditional morphology-based taxonomy, which is a slow, imprecise process, focused on restricted groups of organisms. We envision a new paradigm in ecosystem assessment, which we refer to as ‘Biomonitoring 2.0’. This new schema employs DNA-based identification of taxa, coupled with high-throughput DNA sequencing on next-generation sequencing platforms. We discuss the transformational nature of DNA-based approaches in biodiversity discovery and ecosystem assessment and outline a path forward for their future widespread application.
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            An inordinate fondness? The number, distributions, and origins of diatom species.

            The number of extant species of diatoms is estimated here to be at least 30,000 and probably ca. 100,000, by extrapolation from an eclectic sample of genera and species complexes. Available data, although few, indicate that the pseudocryptic species being discovered in many genera are not functionally equivalent. Molecular sequence data show that some diatom species are ubiquitously dispersed. A good case can be made that at least some diatom species and even a few genera are endemics, but many such claims are still weak. The combination of very large species numbers and relatively rapid dispersal in diatoms is inconsistent with some versions of the "ubiquity hypothesis" of protist biogeography, and appears paradoxical. However, population genetic data indicate geographical structure in all the (few) marine and freshwater species that have been examined in detail, sometimes over distances of a few tens of kilometres. The mode of speciation may often be parapatric, in the context of a constantly shifting mosaic of temporarily isolated (meta) populations, but if our "intermediate dispersal hypothesis" is true (that long-distance dispersal is rare, but not extremely rare), allopatric speciation could also be maximized. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.
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              RIVPACS models for predicting the expected macroinvertebrate fauna and assessing the ecological quality of rivers

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                Author and article information

                Journal
                Metabarcoding and Metagenomics
                MBMG
                Pensoft Publishers
                2534-9708
                December 18 2019
                December 18 2019
                : 3
                Article
                10.3897/mbmg.3.39041
                © 2019

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