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Identifying Bearded and Ringed Seal Diet- a Comparison Of IDENTIFYING BEARDED AND RINGED SEAL DIET- A COMPARISON OF STOMACH CONTENTS, STABLE ISOTOPES, FATTY ACIDS, AND FECAL DNA By Anna Laura Bryan RECOMMENDED: sarahh HMy, PrTT3. Vdjdsefy Committee Member Lori Quakenbush, M.S. Advisory Committee Member Kris Hundertmark, Ph.D. Advisory Committee Co-Chair <& '/i^^&- ^Lara Horstmann-Dehn, PI Advisory Committee Co-Chair k. Diane Wagner, Ph.D. Chair, Department of Biology and Wildlife APPROVED: Paul Layer, Ph.D. Dear^-College of Natural Science and Mathematics ^m^ IDENTIFYING BEARDED AND RINGED SEAL DIET– A COMPARISON OF STOMACH CONTENTS, STABLE ISOTOPES, FATTY ACIDS, AND FECAL DNA A THESIS Presented to the Faculty of the University of Alaska Fairbanks In Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Anna Laura Bryan, B.S. Fairbanks, Alaska August 2014 Title Page Abstract Stomach contents, stable isotopes, fatty acids, and more recently fecal DNA are commonly used to infer the diet of marine mammals. However, how complementary or contradictory these methods are, especially when considering individual diet variability, remains poorly understood. This study assessed the differences in the dietary information resulting from stomach contents, stable isotopes, and fatty acids for adult bearded seals (Erignathus barbatus), and fishes identified from stomach contents and fecal DNA for bearded and ringed seals (Pusa hispida), harvested in Alaska for subsistence use. Stomach contents and fecal DNA provided information on recently consumed prey. In contrast, stable carbon and nitrogen isotopes of muscle and fatty acid profiles of blubber provided information on prey consumed and integrated over a longer time frame, but taxonomic resolution of prey was low. Overall, stomach contents provided the most dietary data, while fecal DNA delivered the least. Using denaturing gradient gel electrophoresis (DGGE) of 16S gene fragments, only 40% of the fecal samples (12 bearded and one ringed seal) produced detectable DNA suitable for reference gene amplification. Only three fish species could be positively identified in the diet of seals (Arctic cod, Boreogadus saida; shorthorn sculpin, Myoxocephalus scorpius; and an unknown snailfish species, Liparidae) when using fecal DNA. In a dietary comparison, and despite differences in dietary time frames, the relative occurrence (RO) of prey from stomach contents and the mean proportions of prey source groups from a Bayesian stable isotope mixing model (SIAR) were similar. The proportions of indicator fatty acids from full-thickness blubber, such as 16:4n-1, 20:5n-3, 20:4n- 6, 20:1n-9, 22:1n-11, and the presence of non-methylene-interrupted fatty acids were similar to other fatty acid studies of bearded seals in Alaska, and suggest a benthic diet. Overall, the methods yielded different, but not necessarily contradictory results. v Table of Contents Page Signature Page ................................................................................................................................. i Title Page ....................................................................................................................................... iii Abstract ........................................................................................................................................... v Table of Contents .......................................................................................................................... vii List of Tables ................................................................................................................................. xi List of Figures .............................................................................................................................. xiii List of Appendices ........................................................................................................................ xv Acknowledgements ..................................................................................................................... xvii Chapter 1: General Introduction ..................................................................................................... 1 Chapter 2: Identifying bearded seal diet – a comparison of individual seals using stomach contents, stable isotopes, and fatty acids ........................................................................................ 9 2.1 Abstract ................................................................................................................................. 9 2.2 Introduction ......................................................................................................................... 10 2.3 Methods ............................................................................................................................... 14 2.3.1 Field Collections ........................................................................................................... 14 2.3.2 Stomach Content Analysis ........................................................................................... 15 2.3.3 Stable Isotope Analysis ................................................................................................ 16 2.3.4 Fatty Acid Analysis ...................................................................................................... 18 2.3.5 Statistical Analysis ....................................................................................................... 19 2.3.6 Stable Isotope Mixing Model ....................................................................................... 20 2.3.7 Method Comparisons.................................................................................................... 22 2.4 Results ................................................................................................................................. 22 2.4.1 Stomach Content Analysis ........................................................................................... 22 2.4.2 Stable Isotope Analysis ................................................................................................ 23 2.4.3 Fatty Acid Analysis ...................................................................................................... 25 vii 2.5 Discussion ........................................................................................................................... 26 2.6 Conclusions ......................................................................................................................... 33 2.7 Acknowledgements ............................................................................................................. 34 2.8 References ........................................................................................................................... 35 2.9 Tables .................................................................................................................................. 44 2.10 Figures ............................................................................................................................... 51 2.11 Appendix ........................................................................................................................... 54 Chapter 3: Fish prey in bearded and ringed seal diet – a comparison of stomach contents and fecal DNA ..................................................................................................................................... 57 3.1 Abstract ............................................................................................................................... 57 3.2 Introduction ......................................................................................................................... 58 3.3 Methods ............................................................................................................................... 61 3.3.1 Sample Collections ....................................................................................................... 61 3.3.2 Stomach Content Analysis ........................................................................................... 62 3.3.3 DNA Extractions .......................................................................................................... 62 3.3.4 PCR Amplifications...................................................................................................... 63 3.3.5 Denaturing Gradient Gel Electrophoresis .................................................................... 66 3.4 Results ................................................................................................................................. 68 3.4.1 Stomach Content Analysis ........................................................................................... 68 3.4.2 DNA-Based Diet Analysis ........................................................................................... 69 3.5 Discussion ........................................................................................................................... 71 3.5.1 Seal Diet ....................................................................................................................... 71 3.5.2 Methods Considerations ............................................................................................... 74 3.6 Conclusions ......................................................................................................................... 77 3.7 Acknowledgements ............................................................................................................
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