دورية أكاديمية
أعرض في EDS

Toward quantitative metabarcoding.

التفاصيل البيبلوغرافية
العنوان: Toward quantitative metabarcoding.
المؤلفون: Shelton AO; Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA., Gold ZJ; Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA.; CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA., Jensen AJ; CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA.; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA., D Agnese E; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA., Andruszkiewicz Allan E; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA., Van Cise A; North Gulf Oceanic Society, Visiting Scientist at Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, Washington, USA., Gallego R; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA.; Departamento de Biologia, Universidad Autonoma de Madrid, Unidad de Genetica, Madrid, Spain., Ramón-Laca A; CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, USA.; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA., Garber-Yonts M; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA., Parsons K; Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA., Kelly RP; School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA.
المصدر: Ecology [Ecology] 2023 Feb; Vol. 104 (2), pp. e3906. Date of Electronic Publication: 2022 Dec 21.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Ecological Society of America Country of Publication: United States NLM ID: 0043541 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1939-9170 (Electronic) Linking ISSN: 00129658 NLM ISO Abbreviation: Ecology Subsets: MEDLINE
أسماء مطبوعة: Publication: Washington, DC : Ecological Society of America
Original Publication: Brooklyn, NY : Brooklyn Botanical Garden
مواضيع طبية MeSH: DNA Barcoding, Taxonomic*/methods , Microbiota*, DNA/genetics ; Ecology ; Biodiversity
مستخلص: Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture-struggle to link genetic observations to the underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology, it becomes more important to develop ways to make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying polymerase chain reaction mechanism explains the observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arise, rather than transforming the data post hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.
(© 2022 The Ecological Society of America. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)
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فهرسة مساهمة: Keywords: amplicon sequencing; bias adjustment; community structure; compositional analysis; diet analysis; environmental DNA
المشرفين على المادة: 9007-49-2 (DNA)
تواريخ الأحداث: Date Created: 20221102 Date Completed: 20230202 Latest Revision: 20230228
رمز التحديث: 20240628
DOI: 10.1002/ecy.3906
PMID: 36320096
قاعدة البيانات: MEDLINE
الوصف
تدمد:1939-9170
DOI:10.1002/ecy.3906