Evaluating the winter diet of a reintroduced herd of elk in the Cumberland Mountains, Tennessee, using next-generation sequencing techniques

A distinct subspecies of elk (Cervus canadensis), the North American elk (C. canadensis canadensis), once inhabited portions of the southeastern United States, including Tennessee, until their extirpation in the mid 1800s. From 2000 to 2008, 201 Manitoban elk were reintroduced on the North Cumberland Wildlife Management Area (NCWMA). A year-long food habits study using histological analysis of plant material from feces was completed for the NCWMA elk from 2003 to 2004 and has since aided managers in their landscape planning. Since then, more elk have been released onto the area, food plots have been established throughout the NCWMA, and the population has had approximately 20 years to establish itself on the landscape. Thus, a reevaluation of dietary habits is warranted. We collected 357 groups of fecal pellets from 68 set openings within the 79,318 ha NCWMA weekly from February to April of 2019 for a winter fecal diet analysis using next-generation sequencing techniques, also referred to as metabarcoding. Metabarcoding is a non-invasive methodology that has proven to be more effective in identifying herbivore diets than previously used methods. We conducted DNA extractions, a two-step polymerase chain reaction protocol, and completed library preparation of the samples using the Illumina MiSeq sequencing protocol to isolate the plant DNA from the other genetic material in the scat. A bioinformatical analysis was then conducted to determine what plants were identified from sequencing. Statistical analyses performed include calculating proportions for the genera detected from sequencing, determining if specific plants were used differently by males and females from specific genetic groups on the NCWMA, investigating alpha and beta diversity of sample sequences, and assessing the use of forage classes by elk during the winter of 2019. The results from this study will further inform managers of the dietary habits of the reintroduced NCWMA herd and assist them in future habitat management.