Spatial and temporal variation in the diet of introduced sambar deer (Cervus unicolor) in an alpine landscape

Context. In south-eastern Australia, the abundance and distribution of non-native sambar deer (Cervus unicolor) has increased dramatically in alpine environments. As a result, significant concern surrounds the potential for the species to impact rare plant species and vegetation communities through browsing.

Aims. We aimed to determine the diversity of the plant species eaten by sambar deer in the Alpine National Park and to understand any spatial and temporal variation in deer diets.

Methods. We collected 90 sambar deer faecal pellet samples over a three-month flowering period across two contrasting study sites with differing elevation, vegetation, and underlying geology. We performed DNA sequencing using the ITS2 gene region and assigned dietary items to the lowest taxonomic level possible. The frequency of occurrence and sequencing read depth of each dietary item were calculated to investigate the diet of sambar deer at spatial and temporal scales, and dietary preferencing was assessed by comparing the frequency of occurrence of dietary items to the observation records for each dietary item in the study area.

Key results. We detected a total of 369 unique plant Operational Taxonomic Units (OTUs) from sambar deer faecal samples, representing 35 families and 80 genera. Considerable variation in the diet was observed over small spatial scales, and evidence of temporal diet variation was noted in one of the study sites. We detected Silky Snow-daisy (Celmisia sericophylla), which is currently listed as critically endangered under the Flora and Fauna Guarantee Act 1988, and Hawkweed (Pilosella spp.), a highly invasive, non-native taxon which is sparingly established in Alpine ecosystems.

Conclusions. Sambar deer displayed an intermediate feeder behaviour in alpine environments, foraging on a variety of forbs and shrubs, however, forbs were the dominant dietary items. The spatial variation observed in the diet of sambar deer suggests that individual deer are unlikely to be dispersing widely while foraging. 

Implications. Our results emphasise the need for careful evaluation of sambar deer impacts within individual sites and at small spatial scales. The detection of species of conservation significance in the diet indicates that the presence of sambar deer should be considered a significant risk to biodiversity in areas of high conservation value.

Methods
The study was conducted on the Bogong High Plains (BHP), within the Alpine National Park, approximately 240 km north-east of Melbourne, Victoria, Australia (36° 50’ S, 147° 20’ E). Within the BHP, two ecologically distinct sites were selected for sampling. These included the alpine Mt Nelse and sub-alpine Basalt Hill study sites. At each of these study sites, collection area for faecal pellet samples was <5 km2. Within each site, sambar deer faecal pellet samples were collected monthly (January to March), from three different vegetation types: snowpatch herbfields, grasslands, and wetlands. A total of 90 faecal pellet group samples were collected (n = 45 at each of the study sites; comprising 15 samples from each month across the three vegetation communities). We stratified the sample collection across each month and within each site, by collecting six groups of faecal pellets from grasslands, five groups from wetlands, and 4 groups from snowpatch herbfields. We opportunistically surveyed the same vegetation types within each site monthly and only collected fresh samples, described as those that were still brown and exhibited a wet shine with no outer decay. 

Each faecal pellet group sample was homogenised and subsampled three times, resulting in a total of 270 samples for DNA extraction. DNA extractions were performed with ~100 mg of faecal sample using a QIAmp Fast DNA Stool Mini Kit (Qiagen) following manufacturer protocols and were eluted in a final volume of 200 μL. Throughout the process, negative extractions containing no faecal material were performed to monitor potential contamination. Each DNA extraction was amplified using the ITS2 gene region of nuclear ribosomal DNA, using the established primer set ITS2-S2F and ITS4. Illumina adaptors and indexing primers were attached following the first round of PCRs, and were then cleaned using an SPRI magnetic bead mix to remove non-specific DNA fragments. Preparation for sequencing was undertaken following the Illumina MiSeq protocol, using a MiSeq Reagent v2 (2 × 250bp) sequencing kit.