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

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.