Abstract

Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce. We used a metabarcoding approach (PCR amplicons of the plant rbcL gene) to survey the diet of white-tailed deer (fecal samples), from a forested site in Warren County, Virginia with a comprehensive plant species inventory and corresponding reference collection of plant barcode and chloroplast sequences. We sampled fecal pellet piles and extracted DNA from 12 individual deer in October 2014. These samples were compared to a reference DNA library of plant species collected within the study area. For 72 % of the amplicons, we were able to assign taxonomy at the species level, which provides for the first time-sufficient taxonomic resolution to quantify the relative frequency at which native and exotic plant species are being consumed by white-tailed deer. For each of the 12 individual deer we collected three subsamples from the same fecal sample, resulting in sequencing 36 total samples. Using Qiime, we quantified the plant DNA found in all 36 samples, and found that variance within samples was less than variance between samples (F = 1.73, P = 0.004), indicating additional subsamples may not be necessary. Species level diversity ranged from 60 to 93 OTUs per individual and nearly 70 % of all plant sequences recovered were from native plant species. The number of species detected did reduce significantly (range 4-12) when we excluded species whose OTU composed <1 % of each sample's total. When compared to the abundance of native and non-natives plants inventoried in the local community, our results support the observation that white-tailed deer have strong foraging preferences, but these preferences were not consistent for species in either class. Deer forage behaviour may favour some exotic species, but not all.

Highlights

  • Trophic interactions among species are thought to be a critical regulatory mechanism affecting species fitness and community composition (Paine 1966; Shears and Babcock 2003)

  • These studies follow the pathway of metagenomic analyses first pioneered in environmental and human microbiome studies of bacteria (Lane et al 1985; Hugenholtz et al 1998), using PCR amplicon data from DNA samples containing a mixture of species, and large reference databases for those genes, notably 16S in microbial communities (Baker and Banfield 2003; Sogin et al 2006; Turnbaugh et al 2009)

  • This study focused on the diet of white-tailed deer (Odocoileus virginianus) at the Smithsonian Conservation Biology Institute (SCBI) in Front Royal, VA, adjacent to the northern end of Shenandoah National Park

Read more

Summary

Introduction

Trophic interactions among species are thought to be a critical regulatory mechanism affecting species fitness and community composition (Paine 1966; Shears and Babcock 2003). Molecular genetic tools to quantify trophic interactions have been explored from a technical perspective (Hibert et al 2013; Ficetola et al 2016) These studies follow the pathway of metagenomic analyses first pioneered in environmental and human microbiome studies of bacteria (Lane et al 1985; Hugenholtz et al 1998), using PCR amplicon data from DNA samples containing a mixture of species, and large reference databases for those genes, notably 16S in microbial communities (Baker and Banfield 2003; Sogin et al 2006; Turnbaugh et al 2009). Numerous reviews have highlighted the utility of these methods in ecology (Valentini et al 2009; Bourlat et al 2013; Clare 2014), and increasing numbers of reports implementing metagenomic methods are being published

Methods
Results
Discussion
Conclusion
Full Text
Paper version not known

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call