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MODELLING ENERGY SEQUESTRATION and FORAGING by HARBOR PORPOISES in SAN FRANCISCO BAY a Thesis Submitted to the Faculty of San Fr

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MODELLING ENERGY SEQUESTRATION and FORAGING by HARBOR PORPOISES in SAN FRANCISCO BAY a Thesis Submitted to the Faculty of San Fr MODELLING ENERGY SEQUESTRATION AND FORAGING BY HARBOR PORPOISES IN SAN FRANCISCO BAY A thesis submitted to the faculty of San Francisco State University A5 In partial fulfillment of 3 6 The Requirements for The Degree b'OL Master of Science In Biology: Ecology, Evolution, and Conservation Biology by Cara Alyse Gallagher San Francisco, California May, 2016 Copyright by Cara Alyse Gallagher 2016 CERTIFICATION OF APPROVAL I certify that I have read Modelling Energy Sequestration and Foraging of Harbor Porpoises in San Francisco Bay by Cara Alyse Gallagher; and that in my opinion that work meets the criteria for approving a thesis submitted in partial fulfillment of the requirements for the degree: Master of Science in Biology: Ecology, Evolution, and Conservation Biology at San Francisco State University. Professor of Geography & Environment MODELLING OF ENERGY SEQESTRATION AND FORAGING OF HARBOR PORPOISES IN SAN FRANCISCO BAY Cara Alyse Gallagher San Francisco, California 2016 The occupation of an ecosystem by a new top predator could affect the stability of a food web. In San Francisco Bay (SF Bay), there is evidence for a multi-decadal disappearance of harbor porpoises {Phocoena phocoena) that spanned from the 1940’s to the early 2000’s. Understanding the energetic role of this predator in the food web, in addition to the conditions that allowed for occupation of the Bay, is crucial to shedding light on the possible impacts of this species and on the state of the ecosystem. Here two modelling approaches were used in order to assess the energetics of harbor porpoises in SF Bay. The first model presented was an equation-based, velocity-dependent energy budget of harbor porpoises. As harbor porpoises have been shown to reproduce on an annual calving cycle in some regions, the minimum cost of transport was found for each possible reproductive state (non-pregnant, non-lactating (NPL)=1.6 J kg'W ; pregnant (P)=1.8 J kg'W ; lactating (L)=3.1 J kg'W 1; and pregnant and lactating (PL)=3.2 J kg'W 1). The total daily costs, in terms of carbon uptake, were then estimated for a NPL porpoise and a PL porpoise (NPL=341.3 g; PL=756.4 g) and when compared using a one-way ANOVA test, the difference was significant (F=15,797, d /= l, p<0.001). The second model presented was an agent-based, ecophysiological model of porpoise foraging in central SF Bay. Energy expenditure was estimated using the swimming speed and the reproductive status of the porpoise agent and energy intake was dependent on foraging success, measured by the capture of anchovy agents in SF Bay. The total daily energetic costs of each reproductive state were found (NPL=8060.4 kJ; P=8776.3 kJ; L= 19269.6 kJ; and PL=19985.6 kJ). The marginal value theorem was used as a test of habitat optimum for harbor porpoises in SF Bay and using the model, it was found that foraging success was more dependent on the number of anchovy schools than the number of anchovies per school. The number of schools that allowed for foraging levels higher than found for wild porpoises for a population of 50 animals foraging inside SF Bay was 41 schools of anchovies. When estimating total energy sequestration by differing numbers of harbor porpoises foraging in SF Bay, competition emerged as a factor influencing foraging success. For 33 and 165 porpoises foraging in SF Bay, total carbon consumed during a 6-hour foraging bout was estimated at 17,111.5 ±1 096.0 and 74,273.5 ± 8171.4 grams of carbon, respectively. As an upper-tropic level species that has recently increased its spatial habitat, it is crucial to investigate the possible impacts of harbor porpoises in San Francisco Bay and these two modelling platforms have allowed for the thorough investigation of the questions proposed. ct representation of the content of this thesis. MtQ} 23, 2oM Ohair, Thesis Committee Daten o t e ‘r ACKNOWLEDGEMENTS I would like to thank all of the amazing people that helped me so much throughout my master’s career. I had never even coded before graduate school, so deciding on a modelling thesis was quite the challenge and I couldn’t have done it without the constant help and support by the people around me. I would first like to express my gratitude, which extends beyond words, to Dr. Jonathan Stern. I would have never thought it possible to have such a knowledgeable and helpful advisor. Thank you so much for guiding and sculpting me into the scientist that I’ve become. I could never thank you enough for all of the idea shooting, stress-calming, and encouraging chats, and of course all of the crab rolls. I hope to continue collaborating far into the future. To the rest of my thesis committee; Dr. Ellen Hines, you have always served as a rock for me in my studies. You have constantly supported me, as well as kept me on track, and I thank you so much for that. One day soon we’ll get that dolphin hung up in RTC! To Dr. Sarah Cohen, I know that serving on the thesis committee of someone studying porpoises wasn’t quite at the top of your to-do list (charismatic megafauna?? Yuck!), but I owe you my thanks for taking me on and I hope to see you around FHL sometime in the future! To my friends and family, I know my work-related craziness has caused me to be a bit of a nut-case from time to time, but I thank you so much for constantly keeping me grounded and reminding me of what’s important. To Laura Duffy, my lab mate and friend, I don’t know how I would have done all this without you. Thank you for always being one step ahead of me and helping me along the way. To Lynette Koftinow, I literally wouldn’t be here if it wasn’t for you! You and the SF Bay chapter of ACS have helped me out so much throughout my academic career, both emotionally and monetarily, and I’m so happy to have you as a friend and colleague. To my incredible boyfriend Paul, thank you so much for your help and support, for talking me through breakdowns, for always reminding me that I can do this, and for sharing your knowledge with me. I know that sometimes my business can be tough for you, but even when it gets in the way of our Magic/Star Trek/vidja games time, you never show it and I’m so grateful for you. To my family, who has supported me in all of my wildest of endeavors, I thank you and love you so much! Our constant phone calls and updates on even the most mundane parts of our lives have meant so much to me. Dad, you have always fostered the scientist in me. I wouldn’t be who I am today without your support, encouragement, and challenging discussions. Mom, your love of animals and nature is what guided me down this path. You are the most incredible woman I have ever met and I am so lucky to have you not only as my mother, but my best friend. You two have always been the first to volunteer in terms of assistance or participation in any experiment I devised and, although you may not really understand what I do on a day-to-day basis, I know that you are so proud and that means the world to me. TABLE OF CONTENTS List of Tables...............................................................................................................................xi List of Figures.............................................................................................................................xii List of Appendices....................................................................................................................xiv Chapter 1: 1. Using models to make predictions......................................................................................... 1 1.1. What are ecological models?...................................................................................1 1.2. Why model?.............................................................................................................. 2 1.3. Modelling challenges..............................................................................................4 1.4. Equation-based versus agent-based ecological modelling.................................5 1.5. Case study: Harbor porpoises in a changing San Francisco B ay ......................7 1.5.1. Overview of approach and objectives...................................................8 1.5.1.1. Objectives................................................................................9 Chapter 2: 2. The metabolic cost of swimming in harbor porpoises, Phocoena phocoena, as predicted by a velocity-based m odel...................................................................................... 11 2.0.1. Abstract ................................................................................................ 11 2.1. Introduction.............................................................................................................12 2.2. Methods................................................................................................................... 16 2.2.1. Model description..................................................................................16 2.2.2. Submodels...............................................................................................16 2.2.2.1. Basal metabolic rate ..............................................................16 22.2.2. Metabolic cost of locomotion........................................... 19 2.2.2.3. Metabolic cost of thermoregulation.................................20 2.2.24. Metabolic cost of reproduction...........................................23 2.2.2.5. Total metabolic cost...........................................................25 2.2.3. Model parameters.................................................................................
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