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The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

Jan Pawlowski 1 Mary Kelly-Quinn 2 Florian Altermatt 3, 4 Laure Apothéloz-Perret-Gentil 1 Pedro Beja 5, 6 Angela Boggero 7, 8 Angel Borja 9 Agnes Bouchez 10 Tristan Cordier 1 Isabelle Domaizon 10 Maria João Feio 11 Ana Filipa Filipe 5, 6 Riccardo Fornaroli 12 Wolfram Graf 13 Jelger Herder 14 Berry van der Hoorn 15 J. Iwan Jones 16 Marketa Sagova-Mareckova 17 Christian Moritz 18 Jose Barquin 19 Jeremy J. Piggott 20, 21 Maurizio Pinna 22 Frédéric Rimet 10 Buki Rinkevich 23 Carla Sousa-Santos 24 Valeria Specchia 22 Rosa Trobajo 25 Valentin Vasselon 10 Simon Vitecek 26, 27, 28 Jonas Zimmerman 29 Alexander Weigand 30, 31 Florian Leese 30 Maria Kahlert 32
Abstract : The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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Jan Pawlowski, Mary Kelly-Quinn, Florian Altermatt, Laure Apothéloz-Perret-Gentil, Pedro Beja, et al.. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Science of the Total Environment, Elsevier, 2018, 637-638, pp.1295-1310. ⟨10.1016/j.scitotenv.2018.05.002⟩. ⟨hal-02629210⟩



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