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Diet Analysis of Pacific Harbour Seals (Phoca Vitulina Richardsi)

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Diet Analysis of Pacific Harbour Seals (Phoca Vitulina Richardsi) DIET ANALYSIS OF PACIFIC HARBOUR SEALS (PHOCA VITULINA RICHARDSI) USING HIGH-THROUGHPUT DNA SEQUENCING by Austen Clouse Thomas B.Sc., Western Washington University, 2004 M.Sc., Western Washington University, 2010 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Zoology) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) September 2015 © Austen Clouse Thomas, 2015 Abstract Harbour seals have long been perceived to compete with fisheries for economically valuable fish resources in the Pacific Northwest, but assessing the amounts of fish consumed by seals requires estimates of harbour seal diets. Unfortunately, traditional diet analysis techniques cannot provide the necessary information to estimate the species, life stage, and biomass of key prey (e.g. salmonids) consumed by seals. I therefore developed a new harbour seal diet analysis methodology, using scat DNA metabarcoding and prey hard-part analysis to create refined estimates of salmon in harbour seal diet. I also sought to understand the quantitative potential of DNA metabarcoding diet analysis (i.e. the relationship between prey biomass proportions and DNA sequence percentages produced by high-throughput amplicon sequencing of seal scat DNA). Analysis of faecal samples (scats) from captive harbour seals fed a constant diet indicated that a wide range of factors influence the numbers of prey sequences resulting from scat amplicon sequencing. These biases ranged from preferential amplification of certain prey species DNA, to sequence quality filtering—in addition to interactions between the various biases. I was able to apply correction factors derived from tissue mixtures of the species fed to captive seals that improved prey biomass estimates from DNA, and found that the lipid content of prey fish species perfectly predicted the magnitude of bias resulting from differential prey digestion. My results suggest that highly accurate pinniped prey biomass estimates can be attained by applying two stages of corrections to prey DNA sequence counts. However applying these corrections to the scats of wild seals is challenging, and requires a complete prey tissue mix library to create species-specific correction factors for all prey. While I established an approach that could be applied to wild seals, a thorough statistical evaluation and follow-up feeding studies are needed to determine if the additional effort is justified for population level diet estimates. Lastly, I developed a decision tree approach for merging salmon DNA and hardparts data from seal scats to determine the species and life stages of salmon consumed by seals in the Strait of Georgia, British Columbia. ii Preface All four data chapters in this thesis are the product of a collaborative effort with other researchers, including scientists at the Australian Antarctic Division, the Washington Department of Fish and Wildlife, Point Defiance Zoo and Aquarium, CSIRO Marine and Atmospheric Research, and the University of British Columbia. While I acknowledge the contributions of all my coauthors, I would like to specifically mention the contributions of Dr. Bruce Deagle to my thesis, who contributed substantially to my research by assisting with study designs, data analysis, and the writing of Chapter 2. Two of the four chapters written as manuscripts have been published in peer-reviewed journals (see below), and the other two are in preparation for submission. Chapter 2. The feeding trial in this chapter was done with collaborators at the Point Defiance Zoo and Aquarium, based on a study design created by Dr. Deagle and myself. I was responsible for the sample processing of harbour seal scat samples and the laboratory analysis of Run 1. I also performed the majority of the data analysis and writing for the first draft manuscript created from the study. After several rounds of peer review, it became clear that additional analyses were needed (including a second sequencing run) to complete the publication, at which point Dr. Deagle took the lead on analyses of the new data. The final accepted publication, which appears in this thesis as Chapter 2, includes both Dr. Deagle and me as the shared primary authors. Dr. Simon Jarman facilitated the work at the AAD and provided manuscript edits. Amanda Shaffer was the primary contact at Point Defiance and coordinated scat collections from the captive seals. For all chapters Dr. Andrew Trites provided manuscript edits and guidance on study designs. This chapter was published in Molecular Ecology Resources in 2013: Deagle BE*, Thomas AC*, Shaffer AK, Trites AW, Jarman SN (2013) Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? Molecular Ecology Resources 13:620-633. [* These authors contributed equally to the study]. Chapter 3. This study developed during the peer review process of my Chapter 2 manuscript, after subsequent analyses of the feeding trial data from the Point Defiance harbour seal scats. The study design, laboratory processing, data analysis and writing of the Chapter 3 manuscript iii were primarily done by me, with significant input from Dr. Deagle. Additionally, Dr. Simon Jarman facilitated the sequencing work at the Australian Antarctic Division and provided manuscript edits. Dr. Katherine Haman contributed conceptual feedback and data interpretation with respect to digestive physiology. An external laboratory (SGS Canada Inc.) performed the proximate composition analysis of seal prey fishes. This chapter was published in a special edition of Molecular Ecology in 2014: Thomas AC, Jarman SN, Haman KH, Trites AW, Deagle BE (2014) Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias. Molecular Ecology 23:3706-3718 Chapter 4. The study design for Chapter 4 was primarily created by me, with input from Dr. Deagle and Dr. Trites. Assistance in the lab was provided by an undergraduate student, Corie Wilson, who graciously spent many hours grinding up fish tissues with me at the UBC Fisheries Centre. I coordinated the molecular sample processing in two external genetics labs (Laboratory for Advanced Genome Analysis, and the UGA Georgia Genomics facility) using protocols adapted from my work with the Australian research group. The manuscript that I wrote from this study also went through several major rounds of revision before taking its final form. Paige Eveson, a statistician at CSIRO, played an integral role in the revision of the manuscript and produced the mathematical expressions contained in the text of the document. All writing and bioinformatic analyses were done by me, with edits and revisions provided by Dr. Deagle and Dr. Trites. This chapter manuscript is in the final stages of preparation and has not yet been submitted for peer review. Chapter 5. Countless hours went into the harbour seal scat collections for this study (~120 collection trips), and would not have been possible without the help of numerous volunteers who assisted me in the field. I did the bulk of the laboratory processing of the scat samples (preparation for molecular and prey bone analysis), with intermittent assistance from undergraduate volunteers. Monique Lance at the Washington Department of Fish and Wildlife performed the morphological identification of prey remains in the seal scat samples – a massive undertaking in itself. Similar to Chapter 4, the molecular wet lab work was subcontracted to an outside laboratory, but all work was directly supervised by me, and done using a protocol that I iv developed for MiSeq sequencing of scat DNA. I performed all bioinformatic and statistical analyses for the study, with some coding assistance provided by Ilai Karen and Alistair Blachford. My fellow PhD student Benjamin Nelson contributed conceptual feedback on the decision tree used to merge data from DNA and prey bone analyses. The writing of the manuscript was done entirely by me, with edits provided by Dr. Bruce Deagle, Dr. Andrew Trites, and Dr. Marc Trudel. Similar to Chapter 4, the manuscript created from this chapter is currently in the final stages of revision and has not yet been submitted for peer review. Animal care and ethics oversight of all research contained herein was administered by the UBC Animal Care Committee under permit # A11-0072. I successfully completed the ethics training requirements of the Canadian Council on Animal Care (CCAC) / National Institutional Animal User Training (NIAUT) Program (Certificate # 4620-11). In addition, all observations of wild harbour seals and collection of seal faeces were done under a Department of Fisheries and Oceans License to Study Marine Mammals for Research Purposes (Permit # MML-2011-10). v Table of contents Abstract .......................................................................................................................................... ii Preface ........................................................................................................................................... iii Table of contents .......................................................................................................................... vi List of tables.................................................................................................................................. xi List of figures ..............................................................................................................................
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