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Toward quantitative metabarcoding.
- Source :
-
Ecology [Ecology] 2023 Feb; Vol. 104 (2), pp. e3906. Date of Electronic Publication: 2022 Dec 21. - Publication Year :
- 2023
-
Abstract
- 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.<br /> (© 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.)
- Subjects :
- DNA genetics
Ecology
Biodiversity
DNA Barcoding, Taxonomic methods
Microbiota
Subjects
Details
- Language :
- English
- ISSN :
- 1939-9170
- Volume :
- 104
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- Ecology
- Publication Type :
- Academic Journal
- Accession number :
- 36320096
- Full Text :
- https://doi.org/10.1002/ecy.3906