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Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

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Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. / Ficetola, Gentile F.; Pansu, Johan; Bonin, Aurélie; Coissac, Eric; Giguet-Covex, Charline; De Barba, Marta; Gielly, Ludovic; Lopes, Carla M.; Boyer, Frédéric; Pompanon, François; Rayé, Gilles; Taberlet, Pierre.

In: Molecular ecology resources, Vol. 15, No. 3, 05.2015, p. 543-556.

Research output: Contribution to journalArticlepeer-review

Harvard

Ficetola, GF, Pansu, J, Bonin, A, Coissac, E, Giguet-Covex, C, De Barba, M, Gielly, L, Lopes, CM, Boyer, F, Pompanon, F, Rayé, G & Taberlet, P 2015, 'Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data', Molecular ecology resources, vol. 15, no. 3, pp. 543-556. https://doi.org/10.1111/1755-0998.12338

APA

Ficetola, G. F., Pansu, J., Bonin, A., Coissac, E., Giguet-Covex, C., De Barba, M., Gielly, L., Lopes, C. M., Boyer, F., Pompanon, F., Rayé, G., & Taberlet, P. (2015). Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular ecology resources, 15(3), 543-556. https://doi.org/10.1111/1755-0998.12338

Vancouver

Ficetola GF, Pansu J, Bonin A, Coissac E, Giguet-Covex C, De Barba M et al. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular ecology resources. 2015 May;15(3):543-556. https://doi.org/10.1111/1755-0998.12338

Author

Ficetola, Gentile F. ; Pansu, Johan ; Bonin, Aurélie ; Coissac, Eric ; Giguet-Covex, Charline ; De Barba, Marta ; Gielly, Ludovic ; Lopes, Carla M. ; Boyer, Frédéric ; Pompanon, François ; Rayé, Gilles ; Taberlet, Pierre. / Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. In: Molecular ecology resources. 2015 ; Vol. 15, No. 3. pp. 543-556.

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@article{5c797a02d1c346b6ba0fb297d37c3e4b,
title = "Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data",
abstract = "Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.",
keywords = "Detectability, Earthworms, False negatives, False-positive detection, Lake sediments, Occupancy modelling, Simulations, Species occurrence",
author = "Ficetola, {Gentile F.} and Johan Pansu and Aur{\'e}lie Bonin and Eric Coissac and Charline Giguet-Covex and {De Barba}, Marta and Ludovic Gielly and Lopes, {Carla M.} and Fr{\'e}d{\'e}ric Boyer and Fran{\c c}ois Pompanon and Gilles Ray{\'e} and Pierre Taberlet",
year = "2015",
month = may,
doi = "10.1111/1755-0998.12338",
language = "English",
volume = "15",
pages = "543--556",
journal = "Molecular ecology resources",
issn = "1755-098X",
publisher = "Wiley-Blackwell",
number = "3",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

AU - Ficetola, Gentile F.

AU - Pansu, Johan

AU - Bonin, Aurélie

AU - Coissac, Eric

AU - Giguet-Covex, Charline

AU - De Barba, Marta

AU - Gielly, Ludovic

AU - Lopes, Carla M.

AU - Boyer, Frédéric

AU - Pompanon, François

AU - Rayé, Gilles

AU - Taberlet, Pierre

PY - 2015/5

Y1 - 2015/5

N2 - Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.

AB - Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.

KW - Detectability

KW - Earthworms

KW - False negatives

KW - False-positive detection

KW - Lake sediments

KW - Occupancy modelling

KW - Simulations

KW - Species occurrence

UR - http://www.scopus.com/inward/record.url?scp=84926466385&partnerID=8YFLogxK

U2 - 10.1111/1755-0998.12338

DO - 10.1111/1755-0998.12338

M3 - Article

AN - SCOPUS:84926466385

VL - 15

SP - 543

EP - 556

JO - Molecular ecology resources

JF - Molecular ecology resources

SN - 1755-098X

IS - 3

ER -