Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

Type Article
Acceptance Date 2021 IN PRESS
Language English
Author(s) Polanco F. AndreaORCID1, Richards Eilísh2, 3, Flück Benjamin2, 3, Valentini Alice4, Altermatt Florian5, 6, Brosse Sébastien7, Walser Jean‐claude2, Eme David8, Marques Virginie9, Manel Stéphanie9, Albouy Camille8, Dejean Tony4, Pellissier LoïcORCID2, 3
Affiliation(s) 1 : Museo de Historia Natural Marina de Colombia (MHNMC) Programa de Biodiversidad y Ecosistemas Marinos Instituto de Investigaciones Marinas y Costeras‐INVEMAR Santa Marta, Colombia
2 : Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich ,Switzerland
3 : Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf, Switzerland
4 : SPYGEN Le Bourget‐du‐Lac, France
5 : Eawag Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology Dübendorf, Switzerland
6 : Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich, Switzerland
7 : Laboratoire Evolution et Diversité Biologique (EDB) Université de Toulouse CNRS ENFA UPS Toulouse, France
8 : Unité Ecologie et Modèles pour l'Halieutique EMH IFREMER Nantes, France
9 : CEFE Univ Montpellier CNRS EPHE‐PSL University IRD Univ Paul Valéry Montpellier 3 Montpellier ,France
Source Environmental DNA (2637-4943) (Wiley) In Press
DOI 10.1002/edn3.232
Keyword(s) biodiversity, biomonitoring, environmental DNA, fishes, in silico PCR, neural network
Abstract

Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish-U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera across Actinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish-U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish-U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness of teleo compared to MiFish-U in tropical and temperate freshwater environments, but that generally both teleo and MiFish-U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection.

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Polanco F. Andrea, Richards Eilísh, Flück Benjamin, Valentini Alice, Altermatt Florian, Brosse Sébastien, Walser Jean‐claude, Eme David, Marques Virginie, Manel Stéphanie, Albouy Camille, Dejean Tony, Pellissier Loïc Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems. Environmental DNA IN PRESS. Publisher's official version : https://doi.org/10.1002/edn3.232 , Open Access version : https://archimer.ifremer.fr/doc/00704/81590/