Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

By Nathan T. Evans, Yiyuan Li, M. Renshaw, Brett P. Olds, K. Deiner, C. Turner, C. Jerde, David M. Lodge, G. Lamberti, M. Pfrender. 2017

190 citations recorded by the source corpus.

Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that ...

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7b97dab856303bfa240a9127926edec41a5d50fe

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Citations in the corpus

Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake (2018, methodology): “…as a complementary or alternative method for monitoring fish in lakes (Jerde, Mahon, Chadderton, & Lodge, 2011; Civade et al., 2016; Hänfling et al., 2016; Lacoursière-Roussel, Côté, Leclerc, & Bernatchez, 2016; Valentini et al., 2016; Evans & Lamberti, 2017; Evans et al., 2017; Hering et al., 2018”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, background): “Additionally, use of more than one locus for a target group can allow for tests of consistency between loci and increase stringency of detection for any species (Evans et al., 2017).”
The Elephant in the Lab (and Field): Contamination in Aquatic Environmental DNA Studies (2020, background): “Metabarcoding studies also commonly remove singletons or doubletons from sequence reads to account for potential low levels of contamination (Evans et al., 2017).”
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish (2020, background): “Since different metabarcoding primers may show divergent taxonomic ranges in amplification, multiple primer sets can be used in combination to increase taxonomic coverage and species detection probability (Evans et al., 2017; Miya et al., 2015; Shaw et al., 2016).”