Presenter: Rowan Batts (University of Alabama)

Description:
Using conserved regions of the mitochondrial genome and second generation sequencing to generate a list of species from a mixed sample, or DNA metabarcoding, is a powerful tool that has been broadly applied in conservation, ecology, and management. DNA metabarcoding can be applied to a wide range of biological and environmental samples. Here, we use this approach to generate relative prey species abundance from killer whale fecal samples to characterize the diet of two different populations of 'resident' fish-eating killer whales in the eastern North Pacific. Understanding the diet of 'resident' killer whales is important for supporting recovery goals for the endangered Southern Resident killer whale population, and informing fisheries management objectives. We compare and contrast the results of an in-house 'Orca' pipeline with the 'Anacapa Toolkit' to generate relative species abundance using genomic DNA extracted from killer whale fecal samples. We quantitatively and qualitatively compare the two pipelines and their output using custom R scripts. Although we observed slight variation in read depth and relative prey species proportions recovered from both pipelines, we ultimately found high concordance in species recovered within each fecal sample resulting in identical ecological conclusions supporting the robustness of the DNA metabarcoding data and our characterization of killer whale diet using this approach. From a limited dataset, these results support previous findings highlighting the significance of salmon in the diet of eastern North Pacific resident killer whales and suggest that, in this case, the ecological conclusions are robust to choice of bioinformatics pipeline.