The utility of DNA based diet analysis in foraging ecology : a case study using a marine generalist predator

In marine ecosystems, identifying what and where animals eat are inferred through indirect methods. These methods are often inadequate and our ability to measure and predict ecological interactions remains poor. The accuracy of diet estimation in marine animals may be improved by the use of DNA based techniques, a potentially valuable but largely untested approach. The predictive power of ecological models may also be improved by synoptic integration of diet with spatially explicit foraging activity. A further gain may be achieved by considering individual variation in foraging behaviour, as reflected by differences in diet and core foraging areas within a population. The objective of this thesis was to investigate the utility of DNA based diet analysis in foraging ecology, explored in the context of top marine generalist predators, southern hemisphere fur seals (Arctocephalus spp.). The effectiveness of DNA based diet analysis for identifying trophic relationships is assessed in a series of captive and field based studies. The diet and foraging activity of individuals in a free-living population are then matched both spatially and temporally, and predator-habitat relationships are modelled with reference to specific predator-prey combinations. The accuracy of DNA based scat analysis for diet estimation was assessed in Arctocephalus seals fed mixed prey diets integrated over several days. This approach was compared with the most commonly used method, morphological scat analysis. Both methods inferred recent diet (within 40 hours), but detection of robust prey consumed was 1.4-5.8 times more likely using genetic analysis than morphological analysis. Presence/absence data was an ineffective quantitative measure of diet using either DNA or morphological methods. Faecal samples from 54 wild lactating Arctocephalus gazella were analysed for prey remains using both DNA and morphological techniques. Morphological analysis implied that nearly all individuals (91%) consumed a monotypic diet, but inclusion of molecular data showed that a large proportion (46%) of seals consumed a more diverse diet DNA based diet analysis identified important predator-prey relationships that were not revealed by morphological analysis. Differences in diet between individuals were mirrored by foraging location data, confirming individual differences in foraging behaviour. Persistent environmental features were significant in describing and predicting core foraging areas, irrespective of diet, suggesting that these areas are likely to be important sources of prey in most years. Monotypic consumers may be more vulnerable in years of poor prey availability. DNA based diet analysis provides a significant contribution to our ability to understand foraging ecology.