Conservation Genetics

, Volume 8, Issue 3, pp 743–747 | Cite as

Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition?

  • Bruce E. Deagle
  • Dominic J. Tollit
Technical Note


We investigate using relative amounts of prey DNA recovered from pinniped faeces to obtain diet composition data. Faeces were obtained from captive sea lions being fed a diet containing three fish species (50%, 36% and 14% by mass). Real-time PCR was used to quantify mtDNA in undigested tissue and in the faecal samples. The percent composition of fish mtDNA extracted from tissue corresponded reasonably well to the mass of fish in the mixture. In faecal samples the absolute amount of fish mtDNA recovered varied 100-fold, but the percent composition of the samples was relatively consistent (57.5 ± 9.3%, 19.3 ± 6.6% and 23.2 ± 12.2%). These results indicate there are prey-specific biases in DNA survival during digestion. However, the biases may be less than those commonly observed in conventional diet studies.


Non-invasive Molecular scatology Steller sea lion Faecal DNA Seal diet 



We thank Nick Gales, Simon Jarman, Mark Hindell and Andrew Trites for valuable advice and their help in the initiation of this project. The project was funded by the Australian Antarctic Division and also supported by the North Pacific Marine Science Foundation through the North Pacific Universities Marine Mammal Research Consortium. We thank the staff at the Vancouver Aquarium Marine Science Centre and members of the UBC Marine Mammal Research Unit for assistance with sample collection. Paige Eveson provided helpful statistical guidance. Work was undertaken in accordance with UBC Animal Care Committee guidelines.


  1. Bowen WD (2000) Reconstruction of pinniped diets: accounting for complete digestion of otoliths and cephalopod beaks. Can J Fish Aquat Sci 57:898–905CrossRefGoogle Scholar
  2. Casper RM, Gales NJ, Hindell MA, Robinson SM (2006) Diet estimation based on an integrated mixed prey feeding experiment using Arctocephalus seals. J Exp Mar Biol Ecol 328:228–239CrossRefGoogle Scholar
  3. Deagle BE, Tollit DJ, Jarman SN, Hindell MA, Trites AW, Gales NJ (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Mol Ecol 14:1831–1842PubMedCrossRefGoogle Scholar
  4. Hogg RV, Tanis EA (2005) Probability and statistical inference, 7th edn. Prentice Hall, New JerseyGoogle Scholar
  5. Jarman SN, Deagle BE, Gales NJ (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Mol Ecol 13:1313–1322PubMedCrossRefGoogle Scholar
  6. Kvitrud MA, Riemer SD, Brown RF, Bellinger MR, Banks MA (2005) Pacific harbor seals (Phoca vitulina) and salmon: genetics presents hard numbers for elucidating predator–prey dynamics. Mar Biol 147:1459–1466CrossRefGoogle Scholar
  7. Laake JL, Browne P, DeLong RL, Huber HR (2002) Pinniped diet composition: a comparison of estimation models. Fish Bull 100:434–447Google Scholar
  8. Miller FJ, Rosenfeldt FL, Zhang CF, Linnane AW, Nagley P (2003) Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: lack of change of copy number with age. Nucleic Acids Res 31:e61PubMedCrossRefGoogle Scholar
  9. Parsons KM, Piertney SB, Middlemas SJ, Hammond PS, Armstrong JD (2005) DNA-based identification of salmonid prey species in seal faeces. J Zool 266:275–281CrossRefGoogle Scholar
  10. Purcell M, Mackey G, LaHood E, Park L, Huber H (2004) Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat. Fish Bull 102:213–220Google Scholar
  11. Sinclair EH, Zeppelin TK (2002) Seasonal and spatial differences in diet in the western stock of Steller sea lions (Eumetopias jubatus). J Mammal 83:973–990CrossRefGoogle Scholar
  12. Symondson WOC (2002) Molecular identification of prey in predator diets. Mol Ecol 11:627–641PubMedCrossRefGoogle Scholar
  13. Tollit DJ, Wong M, Winship AJ, Rosen DAS, Trites AW (2003) Quantifying errors associated with using prey skeletal structures from fecal samples to determine the diet of Steller’s sea lion (Eumetopias jubatus). Mar Mamm Sci 19:724–744CrossRefGoogle Scholar
  14. von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  1. 1.School of ZoologyUniversity of TasmaniaHobart, TasmaniaAustralia
  2. 2.Australian Antarctic DivisionKingston, TasmaniaAustralia
  3. 3.Marine Mammal Research Unit, Fisheries CentreUniversity of British Columbia, AERLVancouverCanada

Personalised recommendations