DNA metabarcoding sequence data for diet analysis of caribou

Woodland caribou (Rangifer tarandus caribou) are threatened in Canada due
to the drastic decline in population size caused primarily by
human-induced landscape changes that decrease habitat and increase
predation risk. Conservation efforts have largely focused on reducing
predators and protecting critical habitat, whereas research on dietary
niches and the role of potential food constraints in lichen-poor
environments is limited. To improve our understanding of dietary niche
variability, we used a next-generation sequencing approach with
metabarcoding of DNA extracted from faecal pellets of woodland caribou
located on Lake Superior in lichen-rich (mainland) and lichen-poor
(island) environments. Amplicon sequencing of fungal ITS2 region revealed
lichen-associated fungi as predominant in samples from both populations,
but amplification at the chloroplast trnL region, which
was only successful on island samples, revealed primary consumption of yew
based on relative read abundance (Taxus spp.; 83.68%) with dogwood (Cornus
spp.; 9.67%) and maple (Acer spp.; 4.10%) also prevalent. These results
suggest that conservation efforts for caribou need to consider the
availability of food resources beyond lichen to ensure successful
outcomes.  More broadly, we provide a reliable methodology for
assessing ungulate diet from archived faecal pellets that could reveal
important dietary shifts over time in response to climate change.