Present address: Sea Mammal Research Unit Ltd, New Technology Centre, North Haugh, St. Andrews, Fife KY 16 9SR, UK.
PERMANENT GENETIC RESOURCES ARTICLE
Proportion of prey consumed can be determined from faecal DNA using real-time PCR
Version of Record online: 18 JAN 2011
© 2011 Blackwell Publishing Ltd
Molecular Ecology Resources
Volume 11, Issue 3, pages 530–540, May 2011
How to Cite
BOWLES, E., SCHULTE, P. M., TOLLIT, D. J., DEAGLE, B. E. and TRITES, A. W. (2011), Proportion of prey consumed can be determined from faecal DNA using real-time PCR. Molecular Ecology Resources, 11: 530–540. doi: 10.1111/j.1755-0998.2010.02974.x
- Issue online: 12 APR 2011
- Version of Record online: 18 JAN 2011
- Received 25 August 2010; revision received 21 November 2010; accepted 25 November 2010
- prey quantity;
- real-time PCR;
- Steller sea lion
Reconstructing the 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. Analysing the soft-matrix of faecal material using DNA-based techniques is an alternative means to identify prey species consumed, but published techniques are largely nonquantitative, which limits their usefulness for some applications. We further developed and validated a real-time PCR technique using species-specific mitochondrial DNA primers to quantify the proportion of prey in the diets of Steller sea lions (Eumetopias jubatus), a pinniped species thought to be facing significant diet related challenges in the North Pacific. We 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. We then applied real-time PCR to DNA extracted from faecal samples obtained from Steller sea lions in captivity that were fed 11 different combinations of herring, eulachon, squid and Pacific ocean perch rockfish (Sebastes alutus), ranging from 7% to 75% contributions per meal (by wet weight). The difference between the average percentage estimated by real-time PCR and the percentage of prey consumed was generally < 12% for all diets fed. Our findings indicate that real-time PCR of faecal DNA can detect the approximate relative quantity of prey consumed for complex diets and prey species, including cephalopods and fish.