How to limit false positives in environmental DNA and metabarcoding?

  title={How to limit false positives in environmental DNA and metabarcoding?},
  author={Gentile Francesco Ficetola and Pierre Taberlet and Eric Coissac},
  journal={Molecular Ecology Resources},
Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positives remains a main challenge for eDNA analyses: in this issue of Molecular Ecology Resources, Lahoz… 

Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model

It is illustrated how the error rates in the eDNA metabarcoding-based species detection can be accounted for by applying the multispecies occupancy modelling framework to study the optimum conditions for molecular experiments.

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

With eDNA methodology becoming increasingly routine, its use is strongly recommended to retrieve species distributional data for SDMs and to improve the data available for a more efficient management.

Improving the reliability of eDNA data interpretation

This work synthesizes recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data and introduces process‐based models and the integration of metabarcoding data as complementing approaches to increase the accuracy of target‐species assessments.

The Elephant in the Lab (and Field): Contamination in Aquatic Environmental DNA Studies

It is found that there has been minimal convergence over time on negative control implementation, methods, and interpretation, which suggests that increased rigor in these smaller, yet critical details remains an outstanding need.


The use of environmental DNA (eDNA) for environmental monitoring has been presented as a technique to replace existing traditional monitoring techniques; being faster, easier and more accurate. In

Studying ecosystems with DNA metabarcoding: lessons from aquatic biomonitoring

The ability of this new technology to improve the quality and utility of ecological data is explored, recognising that the issues raised have widespread applicability across all ecosystem types.

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

This work reviews and synthesizes eDNA studies published to date to highlight the opportunities and limitations of utilizing eDNA in ecology and conservation, and identifies potential ways of reducing limitations in eDNA analysis.

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

A rigorous metabarcoding approach based on a short COI minibarcode and two‐step PCR protocol enabling the “all at once” taxonomic identification of bats and their arthropod prey for several hundreds of samples is detailed.

Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis

The method provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing ‘chirosurveillance’ and conservation strategies and validate 551 COI variants from arthropod.



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

The level of replication required for accurate detection of targeted taxa in different contexts was evaluated and whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false‐positive rates was evaluated.

Improving confidence in environmental DNA species detection

A framework for metagenetic environmental DNA surveillance is provided to foster the confidence of the authors' grandfathers’ fishing prowess by more rigorously evaluating the replication levels necessary to quantify detection errors and ultimately improving their confidence in aquatic species presence.

Statistical approaches to account for false‐positive errors in environmental DNA samples

This work advocates alternative approaches to account for false‐positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false‐ positive errors.

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

A DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate taxa and indicated that primer efficiency is highly species-specific would prevent straightforward assessments of species abundance and biomass in a sample.

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

The results illustrate the potential for eDNA sampling and metabarcode approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data

A computational method is developed that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA and finds that putative wheat DNA is most likely not of ancient origin.

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

A versatile multistrategy decontamination procedure for PCR reagents is developed that allows efficient reagent decontamination while preserving the efficiency of PCR amplification of minute quantities of DNA.

Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification.

It is shown that models that account for possible misidentification have greater support and can yield substantially different occupancy estimates than those that do not and can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur.

Generalized site occupancy models allowing for false positive and false negative errors.

This paper develops a model for site occupancy that allows for both false negative and false positive error rates and provides an analysis of avian survey data using the proposed model and results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.

Long livestock farming history and human landscape shaping revealed by lake sediment DNA.

An approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period shows that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period.