Gradients in richness and turnover of a forest passerine’s diet prior to breeding: a mixed model approach applied to faecal metabarcoding data

Little is known about the dietary richness and variation of generalist
insectivorous species, including birds, due primarily to difficulties in
prey identification. Using faecal metabarcoding we provide the most
comprehensive analysis of a passerine’s diet to date, identifying the
relative magnitudes of biogeographic, habitat and temporal trends in the
richness and turnover in diet of Cyanistes caeruleus (blue tit) along a
39-site, 2° latitudinal transect in Scotland. Faecal samples were
collected during 2014-15 from adult birds roosting in nestboxes
prior to nest building. DNA was extracted from 793 samples and we
amplified COI and 16S minibarcodes. We identified 432 molecular
operational taxonomic units (MOTUs) that correspond to putative dietary
items. Most dietary items were rare, with Lepidoptera being the most
abundant and taxon-rich prey order. We present a novel statistical
approach for estimation of gradients and inter-sample variation in
taxonomic richness and turnover using a generalised linear mixed model. We
discuss the merits of this approach over existing tools and present new
theory and methods for model-based estimation of repeatability.
We find that dietary richness increases significantly as spring advances,
but changes little with elevation, latitude or local tree composition. In
comparison, dietary composition exhibits significant turnover along
temporal and spatial gradients and among sites. Our study shows the
promise of faecal metabarcoding for inferring the macroecology of food
webs, but we also highlight the challenge posed by contamination and make
recommendations of laboratory and statistical practices to
minimise its impact on inference.