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

By Gentile Francesco Ficetola, Johan Pansu, Aurélie Bonin, É. Coissac, C. Giguet-Covex, M. De Barba, Ludovic Gielly, C. M. Lopes, Frédéric Boyer, F. Pompanon and 2 more. Molecular Ecology Resources, 2015

644 citations recorded by the source corpus.

Subfields: Ecological Modeling, Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5e45c929280cf4042c447e7188f5189a0a8d786c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecological Modeling

1. K. Deiner
2. F. Altermatt
3. G. Guillera‐Arroita
4. Caren S. Goldberg
5. C. Turner
6. E. Mächler
7. David S. Pilliod
8. J. Lahoz‐Monfort

In Ecology

1. C. Turner
2. Caren S. Goldberg
3. M. Barnes
4. K. Deiner
5. P. F. Thomsen
6. F. Altermatt
7. David S. Pilliod
8. E. Mächler

In Molecular Biology

1. C. Turner
2. Caren S. Goldberg
3. M. Barnes
4. P. F. Thomsen
5. K. Deiner
6. F. Altermatt
7. David S. Pilliod
8. E. Mächler

Citations in the corpus

• Dealing with false‐positive and false‐negative errors about species occurrence at multiple levels (2017, background): “For instance such errors can be important in aural surveys (McClintock et al. 2010a; Miller et al. 2012b), and in surveys based on the detection of environmental DNA (eDNA; Darling & Mahon 2011; Ficetola et al. 2015; Lahoz-Monfort, Guillera-Arroita & Tingley 2016).”
• Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem (2017, positive): “Nevertheless, for well-characterized faunas, these rates seem likely to bemuch lower than p11 for any given group of interest, and moreover, common quality-control techniques (e.g., Ficetola et al., 2014) likely reduce p10 to near zero.”
• From eDNA to citizen science: emerging tools for the early detection of invasive species (2020, background): “Both false negatives (the failure to detect a target species when actually present) and false positives (the detection of a target species when actually absent) can occur with eDNA surveillance, just as they can for many other monitoring approaches in applied ecology (Ficetola et al. 2015).”
• Assessing the cost‐efficiency of environmental DNA sampling (2016, background): “…7, 1291–1298 depend on the decision context, and on system-specific factors that influence false-positive rates, such as primer and probe specificities, sample collection and preparation protocols and eDNA degradation rates (Ficetola et al. 2015; LahozMonfort, Guillera-Arroita & Tingley 2016).”
• Risk Analysis and Bioeconomics of Invasive Species to Inform Policy and Management (2016, background): “Better statistical estimates of false detection results (117, 118) and improved control technologies can decrease the occurrence of such outcomes.”
• The ecology of environmental DNA and implications for conservation genetics (2016, background): “These include falsepositives and false-negatives (Ficetola et al. 2014), PCR and sequencing errors (Schnell et al. 2015), marker Table 1 continued Environment eDNA target Major findings Citation Laboratory soil mesocosms Transgenic tobacco leaf material and purified plasmid DNA from Nicotina…”
• DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity (2017, background): “increasing the total number of PCR replicates for each sample (Ficetola et al. 2015).”