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Analysis of institutional authors

Gallego Simon, RamonAuthor

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November 7, 2022
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Toward quantitative metabarcoding

Publicated to:ECOLOGY. 104 (2): e3906- - 2023-01-01 104(2), DOI: 10.1002/ecy.3906

Authors: Shelton, Andrew Olaf; Gold, Zachary J; Jensen, Alexander J; Agnese, Erin D; Allan, Elizabeth Andruszkiewicz; Van Cise, Amy; Gallego, Ramon; Ramon-Laca, Ana; Garber-Yonts, Maya; Parsons, Kim; Kelly, Ryan P

Affiliations

CICOES, University of Washington and Northwest Fisheries Science Center, National Marine Fisheries Service, 3737 Brooklyn Ave NE, Seattle, WA, U.S.A. - Author
Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA, U.S.A. - Author
Natl Marine Fisheries Serv, Northwest Fisheries Sci Ctr, Seattle, WA USA - Author
NOAA, Conservat Biol Div, Northwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA 98115 USA - Author
NOAA, North Gulf Ocean Soc, Northwest Fisheries Sci Ctr, Seattle, WA USA - Author
North Gulf Oceanic Society, Visiting Scientist at Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA, USA. - Author
Univ Autonoma Madrid, Dept Biol, Unidad Genet, Madrid, Spain - Author
Univ Washington, CICOES, Seattle, WA USA - Author
Univ Washington, Sch Marine & Environm Affairs, Seattle, WA 98195 USA - Author
Universidad Autonoma de Madrid, Unidad de Genetica, Departamento de Biologia, C/Darwin, 2. 28049 Cantoblanco, Madrid, Spain. - Author
University of Washington, School of Marine and Environmental Affairs, 3707 Brooklyn Ave NE, Seattle, WA, U.S.A. - Author
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Abstract

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provides 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 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 PCR mechanism explains observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arises, 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.This article is protected by copyright. All rights reserved.

Keywords

bias adjustmentbiodiversitycommunitiescommunity structurecompositional analysisdietdiet analysisenvironmental dnaAmplicon sequencingBias adjustmentBiodiversityCommunity structureCompositional analysisDiet analysisDnaDna barcoding, taxonomicEcologyEnvironmental dnaMicrobiota

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal ECOLOGY due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2023, it was in position 32/197, thus managing to position itself as a Q1 (Primer Cuartil), in the category Ecology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 27.1, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-07, the following number of citations:

  • WoS: 50
  • Scopus: 65
  • Europe PMC: 9

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-07:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 137.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 137 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 10.15.
  • The number of mentions on the social network X (formerly Twitter): 13 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United States of America.