Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

By B. Deagle, Austen C. Thomas, Julie C. McInnes, L. Clarke, E. Vesterinen, Elizabeth Clare, Tyler R. Kartzinel, J. Eveson. bioRxiv, 2018

723 citations recorded by the source corpus.

Advances in DNA sequencing technology have revolutionised the field of molecular analysis of trophic interactions and it is now possible to recover counts of food DNA barcode sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer’s diet should we work strictly with datasets summarising the frequency of occurrence of different food taxa, or is it possible to use the relative number of sequences? Both approaches are applied in the dietary metabarcoding literature, but occurrence data is often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. Here, we point out that diet summaries based on occurrence data overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that even with recovery biases incorporated, using relative read abundance (RRA) information can provide a more accurate view of population-level diet in many scenarios. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue to addressing methodological challenges, and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4887eef2db0f3da90d037c03f62de8cfa69d48cf

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Citations in the corpus

Resolving Food-Web Structure (2020, methodology): “These metrics offer complementary information about the intensity of an interaction (Deagle et al. 2019).”
A practical guide to DNA metabarcoding for entomological ecologists (2020, background): “Size-sorting is often used because larger specimens tend to release more DNA and thus dominate the total sequence count in DNA metabarcoding studies (Deagle et al., 2018a).”
Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs (2019, methodology): “Across metabarcoding studies, both RRA and occurrence metrics are commonly used, but both have biases (Deagle et al., 2018).”
DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems (2019, background): “…obtained by using these methodologies are promising since they are less affected by differential digestibility than morphologic methodologies (Deagle et al., 2009; Egeter et al., 2015), so this is still a developing line of research, and ongoing im‐ provements are expected (Deagle et al., 2019).”