DNA metabarcoding quantifies relative abundances of arthropod taxa in
songbird diets: validation with camera-recorded diets
Abstract
Ecological research is often hampered by the inability to quantify
animal diets. Diet composition can be tracked through DNA metabarcoding
of faecal samples, but whether (complex) diets can be quantitatively
determined with metabarcoding is still debated and needs validation
using free-living animals. This study validates that DNA metabarcoding
of faeces can retrieve actual ingested taxa, and most importantly, that
read numbers retrieved from sequencing can also be used to quantify
relative abundances of dietary taxa. Validation was done with the
hole-nesting insectivorous Pied Flycatcher whose diet was quantified
using camera footage. Size-adjusted counts of food items delivered to
nestlings were used to approximate provided biomass of prey orders and
families and subsequently nestling faeces were assessed through DNA
metabarcoding. To explore potential effects of digestion, stomach and
lower intestine samples of freshly collected birds were subjected to DNA
metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I
(COI), we modified published invertebrate COI primers LCO1490 and
HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA
without significant changing the recovery of other arthropod taxa. DNA
metabarcoding retrieved all commonly camera-recorded taxa. Overall, and
in each replicate year (N = 3), the relative abundances of size-adjusted
prey counts and COI read numbers 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. Similarity in
arthropod community composition between stomach and intestines suggested
limited digestive bias. This DNA metabarcoding validation demonstrates
that quantitative analyses of arthropod diet is possible. We discuss the
ecological applications for insectivorous birds.