Dr Andrew Trites
Determining the relative amounts of prey in Steller sea lion (Eumetopias jubatus) diet using real-time PCR.
Determining diets of pinnipeds by visually identifying prey remains recovered in faecal samples is challenging because of differences in digestion and passage rates of hard parts. Analyzing the soft matrix of faecal material using DNA-based techniques is an alternative means to identify prey species consumed, but published techniques are largely non-quantitative, which limits their applicability. I developed and validated a real-time PCR technique using species-specific mitochondrial DNA primers to quantify the diets of Steller sea lions (Eumetopias jubatus).
I first demonstrated that the proportions of prey tissue DNA in mixtures of DNA isolated from four prey species could be estimated within a margin of ~12% of the percent in the mix. These prey species included herring Clupea palasii, eulachon Thaleichthyes pacificus, squid Loligo opalescens and rosethorn rockfish Sebastes helvomaculatus.
I then applied real-time PCR to DNA extracted from faecal samples obtained from Steller sea lions that had been fed 11 different combinations of herring, eulachon, squid and Pacific ocean perch rockfish (Sebastes alutus), ranging from 7-75% contributions to a meal mix (by wet weight). The difference between the average percentage estimated by real-time PCR and the percentage of prey consumed was generally less than 12% for all diets fed when percentages of prey consumed were corrected for differences in mtDNA density among the prey items. My findings indicate that real-time PCR can detect the quantity of prey consumed for a variety of complex diets and prey species, including cephalopods and fish.
Determining the relative amounts of prey in Steller sea lion (Eumetopias jubatus) diet using real-time PCR. Bowles, E. 2009. In Zoology. MSc thesis, University of British Columbia, Vancouver. 54 pages (PDF)