Evidence-based strategies to navigate complexity in dietary DNA metabarcoding: A reply

Area of Science:

• Ecology
• Bioinformatics
• Molecular Ecology

Background:

• Dietary DNA metabarcoding is vital for understanding animal diets and trophic networks.
• Low-abundance sequences in metabarcoding can be errors or genuine biological signals.
• Current abundance filtering methods risk inflating false-negative rates, impacting ecological inferences.

Purpose of the Study:

• To investigate the impact of abundance-filtering on DNA metabarcoding data.
• To provide guidance for simulation studies and sensitivity analyses in ecological research.
• To balance the benefits of removing false positives with the risks of introducing false negatives.

Main Methods:

• Combined a simulation study with an empirical dataset.
• Evaluated the effects of relative read abundance (RRA) thresholds.
• Developed blueprints for simulation and sensitivity analyses.

Main Results:

• Overcorrecting abundance filters can introduce more false negatives than they eliminate false positives.
• False negatives can significantly alter ecological interpretations and network structures.
• Sensitivity analyses are essential for robust ecological inferences.

Conclusions:

• Accurate dietary characterization requires careful consideration of abundance-filtering trade-offs.
• Awareness of both benefits and costs of filtering is critical for reliable ecological data.
• Avoiding overcorrection strengthens confidence in ecological network analyses.