DOI: 10.5061/dryad.rxwdbrvfz
title: Spatial and temporal variation in the diet of introduced sambar deer (Cervus unicolor) in an alpine landscape

description: 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.
description: 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 &lt;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.
description: # Spatial and temporal variation in the diet of introduced sambar deer
 (Cervus unicolor) in an alpine landscape.
 [https://doi.org/10.5061/dryad.rxwdbrvfz](https://doi.org/10.5061/dryad.rxwdbrvfz) These files contain the data generated for 'Spatial and temporal variation in the diet of introduced sambar deer (Cervus unicolor) in an alpine landscape.' ## Description of the data and file structure The data provided are as follows; PresenceAbsenceMatrix.xlsx: Unique OTUs are displayed as rows, and samples are displayed as columns. A value of 1 represents presence of the OTU in the sample, and 0 represents absence. SampleData.xlsx: This spreadsheet provides collection information for each of the samples, including site, month, and vegetation community. TaxonomyTable.xlsx: This spreadsheet provides taxonomy information for each detected OTU, including Class, Order, Family, Genus, Species, and Growth Form. ## Sharing/Access information If there are any issues with accessing the files, or additional information is required, we welcome further discussion. Please e-mail me at [matthew.quin@my.jcu.edu.au](mailto:matthew.quin@my.jcu.edu.au)