DNA metabarcoding provides new insight into the diet of invasive chital deer (Axis axis) in a tropical savanna landscape

The introduction of non-native species into new environments can cause
significant ecological harm, and is considered a major conservation
threat. As populations of invasive species continue to establish and
increase across the globe, novel methods can provide new insights into
their biology, and potentially aid in management. In this study, we
examined the diet of non-native chital deer (Axis axis) in a tropical
savanna environment in northern Australia. Using DNA metabarcoding of
faecal samples, we described the dietary items consumed by 149 individuals
over a two-year sampling period and associated each item with individual
body condition. The DNA metabarcoding method detected significantly more
dietary items consumed by individual chital deer at each of the taxonomic
levels (family, genus, and species) when compared with previous analyses.
We observed marked differences in diet composition across multiple seasons
and sites. Significantly more sequences from the genera
Terminalia, Diospyros, Jasminum, and Hakea were detected in samples
collected from individuals in poor condition during the dry season,
suggesting that a different suite of food resources is being consumed by a
subset of individuals during periods when forage quantity and quality is
low. Most notably, our results indicated that chital are consuming a
browse-dominated diet throughout the year, differing from previous
macroscopy analyses which suggested chital are predominantly grazers
during the wet season in northern Australia. Our findings give support for
the use of DNA metabarcoding to qualitatively assess diet composition
compared to macroscopic analysis and suggest that the restricted
availability of food during the dry season may result in the consumption
of poor quality and detrimental dietary items.