Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system

By J. Shaw, L. Clarke, S. Wedderburn, T. Barnes, L. Weyrich, Alan Cooper. 2016

296 citations recorded by the source corpus.

Jennifer L.A. Shaw, Laurence J. Clarke, Scotte D.Wedderburn, Thomas C. Barnes, Laura S. Weyrich, Alan Cooper

View Paper: https://www.semanticscholar.org/paper/e36ed1eb81b753afeaf587ae68470f060e2558d0

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In Molecular Biology

Citations in the corpus

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).”
Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake (2018, background): “…which the number of sequence reads for a particular species can be heavily biased by differential primer binding (primer bias, Deiner et al., 2017; Elbrecht & Leese, 2015) and/or subsampling of species during library preparation (Leray & Knowlton, 2015; Shelton et al., 2016; Deiner et al., 2017).”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, background): “, 2016), to medium 60–80 bp (Pawlowski et al., 2014; Shaw et al., 2016) and up to 100 bp (Bista et al.”
Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys (2021, background): “Alternatively, eDNA metabarcoding using universal primers can allow multiple species to be rapidly and concurrently identified (Berry et al., 2019; McInerney & Rees, 2018; Shaw et al., 2016; Stein et al., 2014; Thomsen et al., 2016; Yamamoto et al., 2017).”
Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering (2017, methodology): “Lastly, using eDNA metabarcoding, Shaw et al. (2016) de- tected all fish species captured with fyke nets in each of two Australian river systems.”
Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA (2019, background): “be an extremely promising avenue in freshwater biodiversity studies with the capability to collect monumental amounts of data in short periods of time without disrupting ecosystems (Shaw et al., 2016; Nakagawa et al., 2018).”
Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, unknown): “…locus (Hänfling et al., 2016; Kelly et al., 2014a; Port et al., 2016; Stoeckle, Soboleva, & Charlop‐Powers, 2017; Ushio et al., 2018; Yamamoto et al., 2017), and also 16S rRNA (Berry et al., 2017; Bylemans, Gleeson, Hardy, & Furlan, 2018; Jeunen et al., 2018; Shaw et al., 2016; Stat et al., 2018).”
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, background): “environmental DNA (eDNA)), identify multiple taxa simultaneously from diverse types of samples––stomach contents (3), feces (4,5), sediments (6), soil or water (6–8).”
Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA (2017, methodology): “Given the amount of missing diagnostic information in reference databases used for macroorganism taxonomic assignment (Shaw et al., 2016; Trebitz, Hoffman, Grant, Billehus, & Pilgrim, 2015), generating data with this method will allow use of any region of the mitogenome for which data exist to…”
Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA (2020, methodology): “…metabarcoding technique has already been applied in various environments, for example, marine (Port et al., 2016; Yamamoto et al., 2017), lotic (Nakagawa et al., 2018; Shaw et al., 2016), and lentic freshwater environments (Hänfling et al., 2016; Thomsen, Kielgast, Iversen, Wiuf, et al., 2012).”