Waves and flows on coral reefs : dynamical regimes and the role of roughness

Coral reefs worldwide are under significant pressure from anthropogenic stressors, including climate change. The threat is large scale and global, and thus the response must be, too. Scientists address the subject from a myriad of fields such as biology, ecology, chemistry, acoustics, socio-economics, cultural studies, and public policy, to name a few. This dissertation is concerned with the physics of coral reefs, specifically the physics of flows around reefs. Reefs rely on outside forces such as winds, tides, and waves to circulate water and govern their physical environment, and thus, changes in the hydrodynamics can change important environmental parameters such as temperature and nutrient availability. Reefs are complex and no two reefs are the same, and while the study of reef hydrodynamics draws on older, more established fields such as coastal engineering, reefs are not simply oddly shaped beaches, and they pose their unique questions and challenges. One such challenge is the complicated geometry of reefs; steep fore reefs, shallow reef flats, spurs and grooves, channels and lagoons. Another is that reefs are orders of magnitude more rough than a sandy beach. The first part of this dissertation addresses the establishment of a framework to analyze and compare reefs in terms of their dynamical regimes, i.e., the dominant forcing and resulting circulation patterns. In this framework, two end members are suggested; the open reef, which can be described in terms of open channel flow, and the closed reef, which is similar to what we observe on beaches. The first chapter of the dissertation defines these concepts and relies on numerical modeling to support why the distinction is meaningful. Given that roughness is a defining feature of coral reefs compared to other coastal environments, Chapters 2 and 3 address the role of roughness in reef flow and to which extent we can measure roughness in the field. Intuitively, we think of roughness and friction as opposing forces that slow down or impede motion, and thus higher roughness would be a detriment to efficient circulation. However, Chapter 2 shows that for certain reefs, high roughness in fact facilitates efficient flushing and low residence times. The dynamics in this case are that of an open reef. In comparison, a reef with lower roughness (e.g., a reef with high mortality or significant physical damage from a storm) is less efficient at circulating and renewing water. The dynamics in these models were more similar to a closed reef. Having established the importance of roughness, Chapter 3 presents on a two-week study at Salomon Atoll, Chagos, in the Indian Ocean, to investigate how reliable our estimates of roughness are. Presuming that a reef has a roughness parameter associated with it, we should be able to quantify it. Our results should be reproducible and not depend in the exact instrument configuration or method of analysis, i.e., two observers inspecting the same phenomena should come to similar conclusions. We show that across four different, commonly used instrument types, deployed in different locations on the reef, and using multiple analytical approaches, the results are largely independent of the method used. However, the results do show that what one observed depends on where one looks. That is, instruments that measure over a small volume, close to the corals will be influenced by small-scale flow features and measure more local effects, whereas instruments that span the entire water column and average over these fluctuations tend to measure aggregate reef effects. Finally, continuing the reflections of the previous chapter, Chapter 4 is a commentary on methods often used to estimate wave exposure on coral reefs within the oceanographic community. As mentioned previously, coral reefs are complex systems with multifaceted threats that require interdisciplinary solutions spanning life, physical, and social sciences. This chapter challenges the use of a method to estimate wave exposure commonly used in ecology and biology, and largely retired in physical oceanography. However, the intention is not to deter interdisciplinary work, but to encourage the use of newer, more accurate methods to further our understanding of the future of coral reefs

Advisor: Monismith Stephen Gene
Dunbar Robert B.
Fringer Oliver B. (Oliver Bartlett)