FN Archimer Export Format
PT J
TI Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
BT 
AF 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
AS 1:1;2:2,3;3:2,3;4:4;5:5,6;6:7;7:2;8:8;9:9;10:9;11:8;12:4;13:2,3;
FF 1:;2:;3:;4:;5:;6:;7:;8:PDG-RBE-EMH;9:;10:;11:PDG-RBE-EMH;12:;13:;
C1 Museo de Historia Natural Marina de Colombia (MHNMC) Programa de Biodiversidad y Ecosistemas Marinos Instituto de Investigaciones Marinas y Costeras‐INVEMAR Santa Marta, Colombia
   Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich ,Switzerland
   Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf, Switzerland
   SPYGEN Le Bourget‐du‐Lac, France
   Eawag Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology Dübendorf, Switzerland
   Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich, Switzerland
   Laboratoire Evolution et Diversité Biologique (EDB) Université de Toulouse CNRS ENFA UPS Toulouse, France
   Unité Ecologie et Modèles pour l'Halieutique EMH IFREMER Nantes, France
   CEFE Univ Montpellier CNRS EPHE‐PSL University IRD Univ Paul Valéry Montpellier 3 Montpellier ,France
C2 MHNMC, COLOMBIA
   ETH ZURICH, SWITZERLAND
   SWISS FED RES INST WSL, SWITZERLAND
   SPYGEN, FRANCE
   EAWAG, SWITZERLAND
   UNIV ZURICH, SWITZERLAND
   UNIV TOULOUSE, FRANCE
   IFREMER, FRANCE
   UNIV MONTPELLIER, FRANCE
SI NANTES
SE PDG-RBE-EMH
IN DOAJ
TC 0
UR https://archimer.ifremer.fr/doc/00704/81590/86079.pdf
   https://archimer.ifremer.fr/doc/00704/81590/86080.docx
LA English
DT Article
DE ;biodiversity;biomonitoring;environmental DNA;fishes;in silico PCR;neural network
AB 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. 
PY 2021
PD NOV
SO Environmental DNA
SN 2637-4943
PU Wiley
VL 3
IS 6
BP 1113
EP 1127
DI 10.1002/edn3.232
ID 81590
ER

EF