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Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates

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Studying Ecosystems With DNA Metabarcoding : Lessons From Biomonitoring of Aquatic Macroinvertebrates. / Bush, Alex; Compson, Zacchaeus G.; Monk, Wendy A.; Porter, Teresita M.; Steeves, Royce; Emilson, Erik; Gagne, Nellie; Hajibabaei, Mehrdad; Roy, Mélanie; Baird, Donald J.

In: Frontiers in Ecology and Evolution, Vol. 7, 434, 08.11.2019.

Research output: Contribution to journalReview articlepeer-review

Harvard

Bush, A, Compson, ZG, Monk, WA, Porter, TM, Steeves, R, Emilson, E, Gagne, N, Hajibabaei, M, Roy, M & Baird, DJ 2019, 'Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates', Frontiers in Ecology and Evolution, vol. 7, 434. https://doi.org/10.3389/fevo.2019.00434

APA

Bush, A., Compson, Z. G., Monk, W. A., Porter, T. M., Steeves, R., Emilson, E., Gagne, N., Hajibabaei, M., Roy, M., & Baird, D. J. (2019). Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates. Frontiers in Ecology and Evolution, 7, [434]. https://doi.org/10.3389/fevo.2019.00434

Vancouver

Bush A, Compson ZG, Monk WA, Porter TM, Steeves R, Emilson E et al. Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates. Frontiers in Ecology and Evolution. 2019 Nov 8;7. 434. https://doi.org/10.3389/fevo.2019.00434

Author

Bush, Alex ; Compson, Zacchaeus G. ; Monk, Wendy A. ; Porter, Teresita M. ; Steeves, Royce ; Emilson, Erik ; Gagne, Nellie ; Hajibabaei, Mehrdad ; Roy, Mélanie ; Baird, Donald J. / Studying Ecosystems With DNA Metabarcoding : Lessons From Biomonitoring of Aquatic Macroinvertebrates. In: Frontiers in Ecology and Evolution. 2019 ; Vol. 7.

Bibtex

@article{17e786d4b6334b86b6c16836838c6124,
title = "Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates",
abstract = "An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a “big data” revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater sample processing capacity. These advances have the potential to amplify the power of ecological studies to detect change and diagnose its cause, through a methodology termed “Biomonitoring 2.0.” Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, specifically comparing the interpretation of otherwise identical bulk-community samples of freshwater benthic invertebrates. We explore how taxonomic resolution, sample similarity, taxon misidentification, and taxon abundance affect the statistical properties of these samples, but recognize these issues are relevant to applications across all ecosystem types. In conclusion, metabarcoding has the capacity to improve the quality and utility of ecological data, and consequently the quality of new research and efficacy of management responses.",
keywords = "benthic macroinvertebrate, biodiversity observation, community ecology, environmental genomics, freshwater, high-throughput sequencing, taxonomic resolution",
author = "Alex Bush and Compson, {Zacchaeus G.} and Monk, {Wendy A.} and Porter, {Teresita M.} and Royce Steeves and Erik Emilson and Nellie Gagne and Mehrdad Hajibabaei and M{\'e}lanie Roy and Baird, {Donald J.}",
year = "2019",
month = nov,
day = "8",
doi = "10.3389/fevo.2019.00434",
language = "English",
volume = "7",
journal = "Frontiers in Ecology and Evolution",
issn = "2296-701X",
publisher = "Frontiers Media S.A.",

}

RIS

TY - JOUR

T1 - Studying Ecosystems With DNA Metabarcoding

T2 - Lessons From Biomonitoring of Aquatic Macroinvertebrates

AU - Bush, Alex

AU - Compson, Zacchaeus G.

AU - Monk, Wendy A.

AU - Porter, Teresita M.

AU - Steeves, Royce

AU - Emilson, Erik

AU - Gagne, Nellie

AU - Hajibabaei, Mehrdad

AU - Roy, Mélanie

AU - Baird, Donald J.

PY - 2019/11/8

Y1 - 2019/11/8

N2 - An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a “big data” revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater sample processing capacity. These advances have the potential to amplify the power of ecological studies to detect change and diagnose its cause, through a methodology termed “Biomonitoring 2.0.” Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, specifically comparing the interpretation of otherwise identical bulk-community samples of freshwater benthic invertebrates. We explore how taxonomic resolution, sample similarity, taxon misidentification, and taxon abundance affect the statistical properties of these samples, but recognize these issues are relevant to applications across all ecosystem types. In conclusion, metabarcoding has the capacity to improve the quality and utility of ecological data, and consequently the quality of new research and efficacy of management responses.

AB - An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a “big data” revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater sample processing capacity. These advances have the potential to amplify the power of ecological studies to detect change and diagnose its cause, through a methodology termed “Biomonitoring 2.0.” Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, specifically comparing the interpretation of otherwise identical bulk-community samples of freshwater benthic invertebrates. We explore how taxonomic resolution, sample similarity, taxon misidentification, and taxon abundance affect the statistical properties of these samples, but recognize these issues are relevant to applications across all ecosystem types. In conclusion, metabarcoding has the capacity to improve the quality and utility of ecological data, and consequently the quality of new research and efficacy of management responses.

KW - benthic macroinvertebrate

KW - biodiversity observation

KW - community ecology

KW - environmental genomics

KW - freshwater

KW - high-throughput sequencing

KW - taxonomic resolution

U2 - 10.3389/fevo.2019.00434

DO - 10.3389/fevo.2019.00434

M3 - Review article

AN - SCOPUS:85075660747

VL - 7

JO - Frontiers in Ecology and Evolution

JF - Frontiers in Ecology and Evolution

SN - 2296-701X

M1 - 434

ER -