A gene route to diet analysis: Developing High Throughput Sequencing as a Tool for Food web Research and Analysis
1/1/13 - 12/31/14
Person photo Prof Peter Hambäck
Department of Ecology, Environment and Plant Sciences

Progress in the ecological analysis of food webs, of importance in both conservation of endangered species, pest control programs and basic ecological research, is hampered by limitations in the diet analysis for many important species. Many species have no larger diet remains in the gut and traditional gut analysis is not possible. Against this background, the overall objective of this project is to develop methods for automated genomic analysis of diets using Next Generation Sequencing (NGS). The focus will be on diets of organisms where classical diet analysis is not possible, such as spiders. A specific focus will be on methods development, comparing classical Sanger sequencing with NGS techniques, but as applications we will use ecological food web analysis. The methods development aim to identify the different information that can be retrieved using the two methods and the ecological applications aim to delineate food webs and to identify niche differences in closely related species. There are two main challenges in the analysis, that will be a particular target for the project. First, pooling samples enables large scale analysis but may result in the loss of quantitative information. This problem will be approached by comparing the information from the Sanger sequencing and the NGS technique. Second, species identification may be incomplete because prey DNA is not yet available in the libraries. This problem will be resolved when the libraries are expanded and when this data is available then diets may be back-tracked. Meanwhile, we will use two approaches for species delimitation, both standard BLAST techniques for identifying the closest relatives (on a family or genus level) and phylogenetic reconstruction for deriving probability estimates of species (or genus) identity. This will be done using Bayesian approaches developed to delineate species in systematics research.
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Dr Elisabet Weingartner
Ecology (Department of Zoology)