PS 48-16 - DNA metabarcoding of fecal samples provides insight into desert rodent diet partitioning

Thursday, August 10, 2017
Exhibit Hall, Oregon Convention Center
Ellen K. Bledsoe, Samantha M. Wisely and S.K. Morgan Ernest, Wildlife Ecology and Conservation, University of Florida, Gainesville, FL

Resource partitioning between species (e.g., reducing diet overlap), which decreases interspecific competition, is a commonly invoked mechanism facilitating long-term coexistence in similar species. While resource partitioning is foundational in most species coexistence models, it is difficult to quantify diet overlap in animals. Until recently, diet partitioning was primarily assessed using behavioral observation and gut or fecal content analysis. These methods, however, are often impractical and time-intensive, and gut content analysis requires sacrificing the animal. DNA metabarcoding, or the simultaneous identification of multiple species in a single sample, is a new genetic analysis technique that offers an efficient and effective way to determine diet content without intensive observation or fatal sampling. We collected fecal samples from three species of granivorous desert rodents (Chaetodipus penicillatus, Dipodomys merriami, D. ordii) from a long-term experimental site near Portal, Arizona, USA. Samples were amplified using primers for the P6-loop of the chloroplast trnL intron and family-specific internal transcribed space (ITS) markers, then sequenced via high-throughput sequencing. Results were then cross-referenced against a local plant reference library and GenBank.


Our preliminary results show clear differences in rodent diets, both among species and individuals (trnL: C. penicillatus, 69.9% Poaceae, 25.5% Fabaceae; D. merriami, 56.5% Fabaceae, 34.2% Poaceae; D. ordii, 60.7% Poaceae, 36.7% Fabaceae). Additionally, we found that the trnL and ITS primers were successful in identifying different species in the diets. ITS results were particularly useful in more narrowly identifying species in the Poaceae, Asteraceae, and Fabaceae families. Therefore, using both sets of primers is imperative for analyzing the diet of these desert rodents at a high resolution. We conclude that DNA metabarcoding can be used successfully as an effective and efficient non-invasive diet assessment method. In the future, we intend to use DNA metabarcoding to assess how the diet of C. penicillatus changes in the presence or absence of the dominant competitors (Dipodomys sp.) in the system as well as how diets expand or contract temporally with plant productivity in the system. This will eventually allow us to determine the relative importance of biotic (presence of competitors) and abiotic (season variability) on diet overlap in this community.