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dc.contributor.author
Polanco Fernandez, Andrea
dc.contributor.author
Richards, Eilísh
dc.contributor.author
Flück, Benjamin
dc.contributor.author
Valentini, Alice
dc.contributor.author
Altermatt, Florian
dc.contributor.author
Brosse, Sébastien
dc.contributor.author
Walser, Jean-Claude
dc.contributor.author
Eme, David
dc.contributor.author
Marques, Virginie
dc.contributor.author
Manel, Stéphanie
dc.contributor.author
Albouy, Camille
dc.contributor.author
Dejean, Tony
dc.contributor.author
Pellissier, Loïc
dc.date.accessioned
2021-12-17T09:25:04Z
dc.date.available
2021-12-06T17:31:10Z
dc.date.available
2021-12-17T09:25:04Z
dc.date.issued
2021
dc.identifier.issn
2637-4943
dc.identifier.other
10.1002/edn3.232
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/518928
dc.identifier.doi
10.3929/ethz-b-000518928
dc.description.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.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Wiley
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject
biodiversity
en_US
dc.subject
biomonitoring
en_US
dc.subject
environmental DNA
en_US
dc.subject
fishes
en_US
dc.subject
in silico PCR
en_US
dc.subject
neural network
en_US
dc.title
Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
dc.date.published
2021-07-06
ethz.journal.title
Environmental DNA
ethz.journal.volume
3
en_US
ethz.journal.issue
6
en_US
ethz.pages.start
1113
en_US
ethz.pages.end
1127
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.grant
Relative importance of ecological and evolutionary determinants of coral reef fish biodiversity
en_US
ethz.identifier.scopus
ethz.publication.place
Hoboken, NJ
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02722 - Institut für Terrestrische Oekosysteme / Institute of Terrestrial Ecosystems::09553 - Pellissier, Loïc / Pellissier, Loïc
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02722 - Institut für Terrestrische Oekosysteme / Institute of Terrestrial Ecosystems::09553 - Pellissier, Loïc / Pellissier, Loïc
ethz.grant.agreementno
164294
ethz.grant.fundername
SNF
ethz.grant.funderDoi
10.13039/501100001711
ethz.grant.program
Projekte Lebenswissenschaften
ethz.date.deposited
2021-12-06T17:31:12Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2021-12-17T09:25:15Z
ethz.rosetta.lastUpdated
2023-02-06T23:28:03Z
ethz.rosetta.versionExported
true
ethz.COinS
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