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Auteur Marques, V.; Guerin, P.-E.; Rocle, M.; Valentini, A.; Manel, S.; Mouillot, D.; Dejean, T.
Titre Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences Type Article scientifique
Année 2020 Publication Revue Abrégée Ecography
Volume Numéro Pages
Mots-Clés (up) 12S primer; alpha-beta-delta-diversity; biodiversity change; clustering; edna; future; identification; marine; metabarcoding; MOTUs; rare biosphere; reference database
Résumé Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non-invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species of the regional pool, which is rarely met. As an alternative, molecular operational taxonomic units (MOTUs) can be extracted as clusters of sequences. However, the extent to which the diversity of MOTUs can predict the diversity of species across spatial scales is unknown. Here, we used 196 samples along the Rhone river (France) for which the reference database is complete to assess whether a blind eDNA approach can reliably predict the ground-truth number of species at different spatial scales. Using the 12S rDNA teleo primer, we curated and clustered 60 million sequences into MOTUs using a new assembled bioinformatic pipeline. We show that stringent quality filters were necessary to remove artefact noise, notably MOTUs present in a single PCR replicate, which represented 55% of MOTUs (103). Post-clustering cleaning also removed 19 additional erroneous MOTUs and only discarded one truly present species. We then show that the diversity of retained fish MOTUs accurately predicted the local (alpha, r = 0.98) and regional (gamma) ground-truth species diversity (67 MOTUs versus 63 species), but also the species dissimilarity between samples (beta-diversity, r = 0.98). This work paves the way towards extending the use of eDNA metabarcoding in community ecology and biogeography despite major gaps in genetic reference databases.
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Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0906-7590 ISBN Médium
Région Expédition Conférence
Notes WOS:000555293900001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2849
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Auteur Leprieur, F.; Oikonomou, A.
Titre The need for richness-independent measures of turnover when delineating biogeographical regions Type Article scientifique
Année 2014 Publication Revue Abrégée Journal of Biogeography
Volume 41 Numéro 2 Pages 417-420
Mots-Clés (up) Beta diversity; bioregionalization; clustering; compositional dissimilarity; freshwater fishes; species richness; species turnover; β-3 index; βsim index
Résumé
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Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 1365-2699 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 896
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