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Physical Oceanography in Coral Reef Environments: Wave and Mean Flow Dynamics at Small and Large Scales, and Resulting Ecological Implications

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Physical Oceanography in Coral Reef Environments: Wave and Mean Flow Dynamics at Small and Large Scales, and Resulting Ecological Implications PHYSICAL OCEANOGRAPHY IN CORAL REEF ENVIRONMENTS: WAVE AND MEAN FLOW DYNAMICS AT SMALL AND LARGE SCALES, AND RESULTING ECOLOGICAL IMPLICATIONS A DISSERTATION SUBMITTED TO THE DEPARTMENT OF CIVIL AND ENVIRONMENTAL ENGINEERING AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Justin Scott Rogers December 2015 © 2015 by Justin S Rogers. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/fj342cd7577 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Stephen Monismith, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Rob Dunbar I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Oliver Fringer I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Curt Storlazzi Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost for Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii Abstract This dissertation investigates the physical oceanography of coral reef environments, specifically focusing on waves and mean flows at small and large scales. At small scales of order ten to a hundred meters, the role of spur and groove formations and their interaction with surface waves and mean flow is examined. Spur-and-groove formations are found on the fore reefs of many coral reefs worldwide. Although these formations are primarily present in wave-dominated environments, their effect on wave-driven hydrodynamics is not well understood. A two-dimensional, depth- averaged, phase-resolving non-linear Boussinesq model (funwaveC) was used to model hydrodynamics on a simplified spur-and-groove system. The modeling results show that the spur-and-groove formations together with shoaling waves induce a nearshore Lagrangian circulation pattern of counter-rotating circulation cells. We present results from two separate field studies of SAG formations on Palmyra Atoll which show their effect on waves to be small, but reveal a persistent order 1 cm/s depth-averaged Lagrangian offshore flow over the spur and onshore flow over the grooves. This circulation was stronger for larger, directly-incident waves and low alongshore flow conditions, consistent with predictions from modeling. Vertical flow was downward over the spur and upward over the groove, likely driven by alongshore differences in bottom stress and not by vortex forcing. We suggest that the conditions for coral recruitment and growth appear to be more favorable on the spur than the groove due to (1) higher “food” supply from higher mean alongshore velocity, downward vertical velocity, and higher turbulence, and (2) lower sediment accumulation due to higher and more variable bottom shear stress. At large scales of order hundreds of meters to kilometers, the wave and mean flow dynamics of a pacific atoll are investigated. We report field measurements of waves and currents made from Sept-2011 to Jul-2014 on Palmyra Atoll in the Central Pacific that were used in conjunction with a coupled wave and three-dimensional iv hydrodynamic model (COAWST) to characterize the waves and hydrodynamics operant on the atoll. Bottom friction, modeled with a modified bottom roughness formulation, is the significant source of wave energy dissipation on the atoll, a result that is consistent with available observations of wave damping on Palmyra. Indeed observed and modeled dissipation rates are an order of magnitude larger than what has been observed on other, less geometrically complex reefs. At the scale of the atoll itself, strong regional flows create flow separation and a well-defined wake, similar to the classic fluid mechanics problem of flow past a cylinder. Circulation within the atoll is primarily governed by tides and waves, and secondarily by wind and regional currents. Tidally driven flow is important at all field sites, and the tidal phasing experiences significant delay with travel into the interior lagoons. Wave driven flow is significant at most of the field sites, and is a strong function of the dominant wave direction. Wind driven flow is generally weak, except on the shallow terraces. The near bed squared wave velocity, a proxy for bottom stress, shows strong spatial variability across the atoll and exerts control over geomorphic structure and high coral cover. Based on Lagrangian float tracks, the mean age was the best predictor of geomorphic structure and appears to clearly differentiate the geomorphic structures. While high mean flow appears to differentiate very productive coral regions, low water age and low temperature appear to be the most important variables for distinguishing between biological cover types at this site. The sites with high coral cover can have high diurnal temperature variability, but their average weekly temperature variability is similar to offshore waters. The mechanism for maintaining this low mean temperature is high mean advection, which occurs at timescales of a week, and is primarily governed by wave driven flows. The resulting connectivity within the atoll system shows that the general trends follow the mean flow paths; however, some connectivity exists between all regions of the atoll system. v Acknowledgments It is impossible to eloquently and succinctly summarize a journey that has taken the last five years, and to adequately acknowledge all the people who have supported and guided me through this process. Nevertheless, here is an attempt. First I would like to acknowledge my advisor, Stephen, for his work in training me to think like an oceanographer and giving me the opportunities and tools to succeed in academia. I sincerely appreciate not only his scientific brilliance when discussing perplexing questions, but also his loyalty and care for me as a person. I am very grateful for his dedication to connecting me with other influential people in the field, and for supporting me through this process. Secondly, I would like to thank my committee members. Rob Dunbar has been very influential in my time here at Stanford, and I sincerely appreciate the opportunities he has given me to collaborate with others outside of EFML. Oliver Fringer has been my favorite teacher at Stanford, as well as an incredible mentor in modeling and life. Curt Storlazzi has been influential in training me in physical oceanography, and helping me get my first paper published. I sincerely appreciate the collaboration and friendship of Dave Koweek, I could not have done this without him. Spending many long days working on a remote tropical atoll together either makes you sincere friends or bitter enemies, and I am happy to say we are the former! I would also like to acknowledge the following colleagues: Jeff Koseff, Falk Feddersen, Derek Fong, Dave Mucciarone, Brock Woodson, Fiorenza Micheli, Steve Litvin, Nirnimesh Kumar, Alex Sheremet, Amatzia Genin, and everyone from the Reefs Tomorrow Initiative. I am indebted to my master’s advisor, Ken Potter, as well as Chin Wu and John Hoopes at UW - Madison for starting this whole thing by imparting their love of research to me. vi I am very grateful to be a part of the wonderful community of Stanford EFML; I certainly could not have completed this journey without all of them. A few people who have had special influence on this dissertation include Ivy Huang, Maha AlNajjar, Bobby Arthur, Kara Scheu, Mallory Barkdull, Simon Wong, Matt Rayson, Phil Wolfram, Sean Vitousek, Ryan Walter, Franco Zarama, Walter Torres, Mike Squibb, Jamie Dunckley and Sarah Giddings. I also acknowledge the administrative support of Jill Filice, Yusong Rogers, and Marguerite Skogstrom. I am grateful to the US Department of Defense NDSEG fellowship for funding me for the first three years. I was also funded by a grant from the Gordon and Betty Moore Foundation, “Understanding coral reef resilience to advance science and conservation,” and teaching support from the Stanford Department of Civil and Environmental Engineering. On a personal level, this journey has been the most difficult five years of my life. There were many times I did not know if I would be able to complete my degree. I am grateful to have been surrounded by many colleagues mentioned above, but also a community of friends and family who encouraged me to keep pushing forward and pursue my passion even in the face of difficulty and at times outright despair. Coming through difficult times has made me appreciate even more that which is good, true, and beautiful in life, a few of which are love, passion, friendship, and faith. A few people who have been especially influential to me include my parents, my brother Grant, sister Heather, my aunt Nellie and uncle Chuck, my grandmother Lorraine, Minna, Tim and Helga, Fatima, my Christian church community at PBC, especially Matt and Laurice Vitalone, Nii and Jana Dodoo, Brad Powley and Lisa Cram. Finally, my daughter Maya continues to provide such joy, inspiration and fun to life; she makes all of this worthwhile. I would like to dedicate this dissertation to my beloved grandmother, Carol, who always believed the best in me.
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