How quantitative is metabarcoding: A meta‐analytical approach
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to...
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| Vydané v: | Molecular ecology Ročník 28; číslo 2; s. 420 - 430 |
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| Hlavní autori: | , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
England
Blackwell Publishing Ltd
01.01.2019
John Wiley and Sons Inc |
| Predmet: | |
| ISSN: | 0962-1083, 1365-294X, 1365-294X |
| On-line prístup: | Získať plný text |
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| Abstract | Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study. |
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| AbstractList | Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study. Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study. Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study. Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study. |
| Author | Hunter, Ewan Pinnegar, John K. Taylor, Martin I. Creer, Simon Davies, Richard G. Lamb, Philip D. |
| AuthorAffiliation | 4 School of Biological Sciences Bangor University Bangor UK 3 Cefas Lowestoft UK 2 School of Environmental Sciences University of East Anglia Norwich UK 1 School of Biological Sciences University of East Anglia Norwich UK |
| AuthorAffiliation_xml | – name: 1 School of Biological Sciences University of East Anglia Norwich UK – name: 4 School of Biological Sciences Bangor University Bangor UK – name: 3 Cefas Lowestoft UK – name: 2 School of Environmental Sciences University of East Anglia Norwich UK |
| Author_xml | – sequence: 1 givenname: Philip D. orcidid: 0000-0003-3748-8241 surname: Lamb fullname: Lamb, Philip D. email: p.lamb@uea.ac.uk organization: University of East Anglia – sequence: 2 givenname: Ewan surname: Hunter fullname: Hunter, Ewan organization: Cefas – sequence: 3 givenname: John K. surname: Pinnegar fullname: Pinnegar, John K. organization: Cefas – sequence: 4 givenname: Simon surname: Creer fullname: Creer, Simon organization: Bangor University – sequence: 5 givenname: Richard G. surname: Davies fullname: Davies, Richard G. organization: University of East Anglia – sequence: 6 givenname: Martin I. orcidid: 0000-0002-3858-0712 surname: Taylor fullname: Taylor, Martin I. organization: University of East Anglia |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30408260$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | 2018 The Authors. Published by John Wiley & Sons Ltd 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. Copyright © 2019 John Wiley & Sons Ltd |
| Copyright_xml | – notice: 2018 The Authors. Published by John Wiley & Sons Ltd – notice: 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. – notice: Copyright © 2019 John Wiley & Sons Ltd |
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| DOI | 10.1111/mec.14920 |
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| SubjectTerms | biomass Deoxyribonucleic acid DNA DNA barcoding Ecological monitoring Environmental DNA high‐throughput sequencing Meta-analysis metabarcoding Moderators next‐generation sequencing Sequences Special Issue: Species Interactions, Ecological Networks and Community Dynamics uncertainty variance |
| Title | How quantitative is metabarcoding: A meta‐analytical approach |
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