ArticleMolecular ecology2019
Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?
Article in Molecular ecology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 262 papers.
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Who cites it
262 citing papers in PubMed.
- Citizen Sailors Provide a Detailed Map of Open-Ocean Surface Biodiversity and Help Link eDNA Data to Satellite Observations.Molecular ecology · 2026Article
- Accounting for Variability Across Years, Depths, and Non-Target Reads Improves Quantification of Root Community Composition in Plant Mixtures.Molecular ecology resources · 2026Article
- Soil Moisture and Prey Life Cycles Promote Seasonal Dietary Shift in a Grassland-Breeding Migratory Shorebird.Ecology and evolution · 2026Article
- Dual-Locus Metabarcoding Reveals Dry-Season Dietary Differentiation Between Elephants and Impalas in a South African Savanna.Ecology and evolution · 2026Article
- Plant species identification by genome skimming across the vascular plant tree of life.The New phytologist · 2026Article
- Opportunistic Feeding and Parasite Assemblages in Sei Whales (Ecology and evolution · 2026Article
- Using next-generation sequencing to unravel the diet composition of Burrowing Parrots over the annual cycle.Die Naturwissenschaften · 2026Article
- A Noninvasive Fecal-DNA Detection Method for Sarcoptic Mange in the San Joaquin Kit Fox (Animals : an open access journal from MDPI · 2026Article
- Biomonitoring 3.0: Beyond Taxa Lists to Evidence-Tiered Monitoring of Ecosystem Dynamics and Interactions.Ecology and evolution · 2026Review
- Article
- Understanding biological control function and trophic interaction dynamics of an artificially released predatory bug by DNA metabarcoding.Insect science · 2026Article
- High trophic niche overlap between sympatric peacock basses (Cichliformes: Cichlidae: Cichla): Concordant findings from three dietary analysis methods.Journal of fish biology · 2026Article
- DNA metabarcoding reveals dietary niche partitioning among threatened Himalayan Ungulates based on chloroplast rbcL and nuclear ITS2 markers.BMC ecology and evolution · 2026Article
- Enhancing the 12S rRNA reference library of South African chondrichthyans to aid in eDNA metabarcoding.BMC zoology · 2026Article
- Spatial Complexity and Rare-Taxon Turnover Structures Benthic Coral Reef eDNA Communities.Molecular ecology · 2026Article
- Diet Metabarcoding Reveals Correlations Between the Consumption of Slugs and Hepatic Toxicants in European Hedgehogs (Erinaceus europaeus).Integrative zoology · 2026Article
- Impacts of large herbivores on savanna plant communities: Predictive models of herbivore selectivity and plant response.Ecology · 2026Article
- Comparing Accuracy and Biases of DNA Metabarcoding, Hybridization Capture, and Metagenomic Sequencing for Quantifying Herbivore Diets.Molecular ecology resources · 2026Article
- Predictors and consequences of diet composition in a declining generalist aerial insectivore.Oecologia · 2026Article
- Habitat-Associated Dietary Plasticity in the Japanese Weasel (Animals : an open access journal from MDPI · 2026Article
202 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA 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 data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often 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 using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. 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 addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.
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