Metabarcoding and Metagenomics 2: 1–17 DOI 10.3897/mbmg.2.22467 Research Article Dropping Hints: Estimating the diets of livestock in rangelands using DNA metabarcoding of faeces Timothy R. C. Lee1, Yohannes Alemseged2, Andrew Mitchell1 1 Australian Museum, Sydney, Australia. 2 NSW Department of Primary Industries, Trangie, Australia. Corresponding author: Timothy R. C. Lee (
[email protected]) Academic editor: Emre Keskin | Received 23 November 2017 | Accepted 17 February 2018 | Published 14 March 2018 Abstract The introduction of domesticated animals into new environments can lead to considerable ecological disruption, and it can be difficult to predict their impact on the new ecosystem. In this study, we use faecal metabarcoding to characterize the diets of three ruminant taxa in the rangelands of south-western New South Wales, Australia. Our study organisms included goats (Capra aega- grus hircus) and two breeds of sheep (Ovis aries): Merinos, which have been present in Australia for over two hundred years, and Dorpers, which were introduced in the 1990s. We used High-Throughput Sequencing methods to sequence the rbcL and ITS2 genes of plants in the faecal samples, and identified the samples using the GenBank and BOLD online databases, as well as a reference collection of sequences from plants collected in the study area. We found that the diets of all three taxa were dominated by the family Malvaceae, and that the Dorper diet was more diverse than the Merino diet at both the family and the species level. We conclude that Dorpers, like Merinos, are potentially a threat to some vulnerable species in the rangelands of New South Wales.