Data from: Who’s for dinner? High-throughput sequencing reveals bat diet differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed

An understanding of species’ diets can aid in conservation and management, but gathering dietary data from predatory species, such as insectivorous bats, often presents logistical challenges. However, recent advances in molecular technologies have enabled the examination of diet by extracting DNA from food remains in either gut or faecal samples. High-throughput sequencing (HTS) allows the analyses of complex, heterogeneous mixtures of DNA, revealing otherwise undetected prey items. To determine the effectiveness of HTS in identifying the dietary ecologies of three insectivorous bat species in the biodiversity hotspot of south-western Australia, we used HTS and bioinformatics analyses to phylogenetically group DNA sequences into Operational Taxonomic Units (OTUs). OTUs were matched against genetic reference databases for prey identification and used for comparing diet diversity, irrespective of taxonomic assignment. HTS revealed 12 prey orders, a greater number than detected using morphological methods and included prey of varying digestibility. Although there was no difference in the number of prey orders consumed across the three bat species, examination at a finer taxonomic resolution yielded significant differences in OTU diversity between the three bat species. Thus, we identified differences in bat diets in a region with high prey diversity and a depauperate reference database, in which the resolving power of HTS can be limited. Irrespective of taxonomy, HTS is a valuable tool for determining dietary differentiation. Allowing cost-effective assessments of diversity in biodiverse regions, HTS may focus future research efforts, such as barcoding projects, by concentrating resources where phylogenetically distinct OTUs occur.