DNA metabarcoding of storage ethanol and conventional morphometric identification of stream macroinvertebrates (New Brunswick, Canada)
Notice bibliographique
Résumé
Stream macroinvertebrates were collected in 15 forest streams in northern New Brunswick, Canada. Within Black Brook (BB), we selected 12 low order streams and their respective catchment areas, which represented a gradient in forest harvesting intensity. The second location was in the unmanaged forest of Mount Carleton Provincial Park (MC) where three headwater streams were sampled. Invertebrates were collected by electroshocking (3 passes of 20 seconds separated by 10-second breaks) within a 100-cm long x 25-cm wide rectangular metal frame; then, five rocks within the rectangle were chosen and carefully inspected to capture attached macroinvertebrates which were added to the sample. This sampling procedure was repeated for 3 different stream riffles with one each at the upstream, middle and downstream sections of the 60-m sampling reach constituting subsamples. In the lab, aquatic insects were identified to genus, with the exception of Chironomidae and Simuliidae – which were identified to family, and classified according to their functional feeding group (FFG) using Merritt et al. (2008). Then, one piece of tissue (usually one leg, but the anterior or posterior end of the body in the case of Dipterans) was pulled from each individual and transferred into a single glass vial filled with 95% ethanol to form a pooled composite for each subsampling site and subsequently submitted for DNA metabarcoding analysis. Attached are the results of these conventional morphometric identifications (stream, replicate, order, family, genus, functional feeding group and number of individuals). DNA was isolated from the preservative ethanol and two fragments (BR5 and F230R) of the cytochrome C oxidase subunit 1 gene were amplified from each sample through a one-stage PCR. Bioinformatic methods involved processing sequence reads obtained from each subsample. Taxonomic assignments were performed using the stand-alone Ribosomal Database Classifier 2.12 with the CO1 Eukaryote v2 training set and they were only used if they met minimum bootstrap support cut-offs: genus bootstrap proportion (BP) >= 0.50, family BP >= 0.30, order BP >= 0.10.The final taxonomy table and FASTA file of exact sequence variants are included within the DNA metabarcoding folder. Using these two datasets, we compared stream macroinvertebrate community metrics based on conventional morphometrics vs. non-destructive DNA metabarcoding from storage ethanol to assess forest management impacts on headwater streams across a gradient of intensively managed forest catchments in eastern Canada. The two approaches demonstrated substantial congruence in the detection of taxa, but DNA metabarcoding from preservative ethanol identified significantly fewer genera (3.3 on average) and families (2.0) than conventional morphometrics. Further details on methods and results can be found in the associated article.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,001 |
| Méta-épidémiologie (sens large) | 0,001 | 0,000 |
| Bibliométrie | 0,001 | 0,002 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,001 |
| Science ouverte | 0,003 | 0,001 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,001 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».