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Data from: DNA metabarcoding successfully quantifies relative abundances of arthropod taxa in songbird diets

Citation

Verkuil, Yvonne (2021), Data from: DNA metabarcoding successfully quantifies relative abundances of arthropod taxa in songbird diets, Dryad, Dataset, https://doi.org/10.5061/dryad.jm63xsj92

Abstract

1. Ecological research is often hampered by the inability to quantify animal diets. Large-scale changes in arthropod diversity, abundance and phenologies urge the need to understand the consequences for trophic interactions. Diet composition of insectivorous predators can be tracked through DNA metabarcoding of faecal samples, but to validate the quantitative accuracy of metabarcoding, validation using free-living animals for which their diet can be approximated, is needed.

2. This validation study assesses the use of DNA metabarcoding in quantifying diets of an insectivorous songbird. Using camera footage, we documented food items delivered to nestling Pied Flycatchers Ficedula hypoleuca, and subsequently sequenced the Cytochrome Oxidase subunit I (COI) in their faeces. Our special interest was to retrieve the relative contribution of arthropod taxa with a PCR-based protocol.

3. Assessment of taxonomic coverage of the invertebrate COI primers LCO1490 and HCO1777, previously applied in insectivorous songbirds, demonstrated that COI barcodes were predominantly assigned to arthropod taxa, however, substantial amounts of reads (2-60%) were assigned to flycatchers. Modified primers reduced vertebrate reads to 0.03%, and yielded more spider DNA without significant changing the recovery of other arthropod taxa.

4. To explore digestive biases, contents of stomachs and lower intestines were compared in eight adult male flycatchers, victims of competitors for nest boxes. Similarity in arthropod community composition between stomach and intestines confirmed limited digestive bias.

5. With nest box cameras in 2013, 2015 and 2016, size-adjusted counts of prey items fed to nestlings were recorded, to approximate provided biomass of arthropod orders and families which allowed comparison with abundance of COI barcode reads in nestling faeces. The relative abundances of size-adjusted prey counts and COI reads correlated at R = 0.85 (CI:0.68-0.94) at order level and at R=0.75 (CI:0.67-0.82) at family level. Each common order and all common taxa within Lepidoptera, Diptera and Coleoptera were retrieved in similar proportions, while the taxonomic resolution was higher in barcodes than in camera records.

6. This DNA metabarcoding validation demonstrates that quantitative arthropod diet analyses is possible in songbirds. We discuss the ecological application of our approach in approximating the arthropod diets in insectivorous birds.

Methods

DNA metbarcoding of faeces.

Raw reads processed with USEARCH.

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Award: ALWOP.2014.109.

Gratama Stichting, Award: 2016-05