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Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies.

ABSTRACT: As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species' true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.

SUBMITTER: Kelly RP

PROVIDER: S-EPMC6702206 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies.

Kelly Ryan P RP Shelton Andrew Olaf AO Gallego Ramón R

Scientific reports 20190820 1

As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species' true biomass abundances poorly or not at all. Here, we use a set of simulations to d ...[more]

PMID: 31431641

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Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies.

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Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies.

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