Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences - Université de Montpellier Accéder directement au contenu
Article Dans Une Revue Ecography Année : 2020

Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences

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.
Fichier principal
Vignette du fichier
Ecography - 2020 - Marques - Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering.pdf (3.37 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

hal-03411045 , version 1 (02-06-2022)

Licence

Paternité

Identifiants

Citer

Virginie Marques, Pierre-Edouard Guerin, Mathieu Rocle, Alice Valentini, Stephanie Manel, et al.. Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences. Ecography, 2020, pp.1779-1790. ⟨10.1111/ecog.05049⟩. ⟨hal-03411045⟩
55 Consultations
35 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More