Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

Knowledge of how animal species use food resources available in the
environment increases our understanding of ecological processes. However,
obtaining this information using traditional methods is a hard task for
species feeding on a large variety of food items in highly diverse
environments. We amplified the DNA of plants for 306 scat and 40 soil
samples, and applied an eDNA metabarcoding approach to investigate food
preferences, degree of diet specialization and diet overlap of seven
herbivore rodent species of the Ctenomys genus distributed in southern and
midwestern Brazil. The metabarcoding approach revealed that species
consume more than 60% of the plant families recovered in soil samples,
indicating generalist feeding habits of ctenomyids. The Poaceae family was
the most common food resource retrieved in scats of all species as well in
soil samples. Niche overlap analysis indicated high overlap in the plant
families and Molecular Operational Taxonomic Units consumed, mainly among
the southern species. Interspecific difference in diet composition was
influenced, among other factors, by the availability of resources in the
environment. In addition, our results provide support for the hypothesis
that the allopatric distributions of ctenomyids allow them to exploit the
same range of resources when available, possibly because of the absence of
interspecific competition.