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