دورية أكاديمية
Signal and noise in metabarcoding data.
| العنوان: | Signal and noise in metabarcoding data. |
|---|---|
| المؤلفون: | Gold Z; Cooperative Institute for Climate, Ocean, & Ecosystem Studies, UW, Seattle, Washington, United States of America.; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., Shelton AO; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., Casendino HR; School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America., Duprey J; School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America., Gallego R; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., Van Cise A; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., Fisher M; School of Aquatic Fisheries Science, UW, Seattle, Washington, United States of America., Jensen AJ; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., D'Agnese E; School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America., Andruszkiewicz Allan E; School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America., Ramón-Laca A; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., Garber-Yonts M; School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America., Labare M; Scripps Institution of Oceanography, UCSD, La Jolla, California, United States of America., Parsons KM; Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America., Kelly RP; School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America. |
| المصدر: | PloS one [PLoS One] 2023 May 11; Vol. 18 (5), pp. e0285674. Date of Electronic Publication: 2023 May 11 (Print Publication: 2023). |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: San Francisco, CA : Public Library of Science |
| مواضيع طبية MeSH: | DNA Barcoding, Taxonomic*/methods , DNA, Environmental*, DNA/genetics ; Polymerase Chain Reaction/methods ; Uncertainty ; Biodiversity |
| مستخلص: | Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing-both of which we can model-but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets. Competing Interests: Authors have no conflicts of interest to report. (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.) |
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| المشرفين على المادة: | 9007-49-2 (DNA) 0 (DNA, Environmental) |
| تواريخ الأحداث: | Date Created: 20230511 Date Completed: 20230515 Latest Revision: 20230615 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC10174484 |
| DOI: | 10.1371/journal.pone.0285674 |
| PMID: | 37167310 |
| قاعدة البيانات: | MEDLINE |
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