Using DNA to explore predator diet in temperate marine ecosystems

This thesis describes the utility of molecular techniques to detect and identify predator/prey interactions in temperate marine ecosystems with an emphasis on the southern rock lobster, (Jasus edwardsii) in Tasmania. A range of DNA-based methods are developed and implemented to better understand the role of this important benthic predator in shaping reef communities. The design and testing of numerous general and species-specific PCR primers is detailed and the utility of these PCR-based assays for monitoring trophic interactions is explored. Captive feeding experiments examine the efficacy of single-species-specific prey detection assays for detection of predation by southern rock lobsters (Jasus edwardsii), and also determine the longevity of the DNA signal and the possibility of quantitative PCR to infer the relative amount of prey consumed by these decapod crustaceans. Based upon these results, the molecular methodologies were tested in a large scale manipulative field experiment to investigate the predation capacity of southern rock lobsters on sea urchins (Centrostephanus rodgersii and Heliocidaris erythrogramma) to understand the shaping of benthic habitats via rock lobster predation in the wild. The results of the dietary component of this experiment are presented and the implications for management are explored briefly. To understand the role of Jasus edwardsii in the marine environment, a broad scale molecular prey inventory approach was used to determine the overall diet of southern rock lobsters both spatially at fished and unfished locations and temporally at sites over several years in Tasmania by using molecular cloning and the use of the 454 Next Generation / pyrosequencing platform. The results of these southern rock lobster prey inventories are presented as well as several other examples of situations with other marine animals using related applications of molecular dietary methods where prey information is difficult to obtain (cephalopods) or is problematic due to the challenges of capturing predators (elasmobranchs). Also provided is a critical review of the utility of molecular prey detection in examining the diet of marine crustaceans, cephalopods and chondrychthians and the thesis concludes by summarising the benefits and pitfalls in using DNA-based dietary methods to address both specific predator-prey issues and more general broad scale trophic webs.