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The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth?
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  • Jordan Cuff,
  • James Kitson,
  • David Hemprich-Bennett,
  • Maximillian Tercel,
  • Samuel Browett,
  • Darren Evans
Jordan Cuff
Newcastle University

Corresponding Author:[email protected]

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James Kitson
Newcastle University
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David Hemprich-Bennett
Oxford University
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Maximillian Tercel
Cardiff University
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Samuel Browett
University of Salford
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Darren Evans
Newcastle University
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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.
28 Apr 2022Submitted to Molecular Ecology Resources
18 May 2022Submission Checks Completed
18 May 2022Assigned to Editor
02 Jun 2022Reviewer(s) Assigned
02 Aug 2022Review(s) Completed, Editorial Evaluation Pending
10 Aug 2022Editorial Decision: Revise Minor
11 Aug 2022Review(s) Completed, Editorial Evaluation Pending
11 Aug 20221st Revision Received
24 Aug 2022Editorial Decision: Accept
Jan 2023Published in Molecular Ecology Resources volume 23 issue 1 on pages 41-51. 10.1111/1755-0998.13705