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The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth?

Lookup NU author(s): Dr Jordan CuffORCiD, Dr James Kitson, Professor Darren Evans



This is the authors' accepted manuscript of an article that has been published in its final definitive form by Wiley-Blackwell Publishing Ltd., 2023.

For re-use rights please refer to the publisher's terms and conditions.


Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed ‘the predator problem’. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multi-predator-taxon studies. We suggest that multi-primer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multi-taxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.

Publication metadata

Author(s): Cuff JP, Kitson JJN, Hemprich-Bennett D, Tercel MPTG, Browett SS, Evans DM

Publication type: Article

Publication status: Published

Journal: Molecular Ecology Resources

Year: 2023

Volume: 23

Issue: 1

Pages: 41-51

Print publication date: 01/01/2023

Online publication date: 26/08/2022

Acceptance date: 24/08/2022

Date deposited: 30/08/2022

ISSN (print): 1755-098X

ISSN (electronic): 1755-0998

Publisher: Wiley-Blackwell Publishing Ltd.


DOI: 10.1111/1755-0998.13705

ePrints DOI: 10.57711/a3ap-h880


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