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This chapter examines the history of coral reef science by drawing on the work of the feminist science studies scholar Donna Haraway. This history moves from early British preoccupations with coral structure, which had reefs as a sort of architecture, to anthropological visions of coral as a metaphor for culture, to reproductive ecological fascinations with the spawning sexways of corals, to contemporary readings of coral genomes for signs of reef health in the age of warming and acidifying seas. The chapter uses Haraway's notion of the “figure” to highlight change and continuity in coral science. It argues that coral reefs can attune their human visitors and inquisitors to empirical and epistemological questions of scale and context— where context, drawing upon a once-upon-a-time literal, but now more figurative, meaning, refers to a “weaving together.”

This chapter explores the diversity of coral reefs and atolls and the factors governing their patterns of distribution. It highlights the important reasons for studying and mapping coral reefs, and describes the major factors that threaten the coral reef ecosystem. Reef ecosystems are now facing overexploitation brought about by sophisticated technology that supports intense fishing and collecting of corals and mollusks. Another threat to coral reefs is coral bleaching, or the loss of photosynthesizing symbionts due to progressive global warming.

Chapter 2, ““And Then We Wept”: Coral Death on Record,” documents the despair side of the pendulum as it contemplates the existing modes and technologies for recording coral bleaching and death. Here, the trajectory is typically of devastation and gloom, as the numbers are depressing at best. Much of the chapter focuses on the third global bleaching event at the Great Barrier Reef, documenting how scientists have both recorded and narrated this event to themselves and to the general public. I examine the role of monitoring in particular, considering whether enhancing scientific knowledge about corals through monitoring is an act of hope, in that it supports conservation action, or one of despair, as it stifles such action and masks the resulting inaction with more and more monitoring. Finally, the chapter shows that even in the world of numbers and maps, “bright spots” and optimistic indexes still rear their more hopeful heads.

This chapter describes ecology of the Galapagos rocky reef system and the important role of biogeographic position on biodiversity, the El Niño cycle, and the history of resource extraction on the current state of the ecosystem. The chapter presents a model of the energetic pathways in the ecosystem and its predictions for fisheries yields and the role of key species. The history of exploitation is outlined as well as the role of the current marine protected areas to develop sustainable management system.

The Philippines depends on its coastal coral reef fisheries as a critical source of livelihood and seafood for both export and domestic consumption. By the mid-1990s, these fisheries had been over-exploited by both large-scale commercial and small-scale subsistence fishermen. Nearly all the coastal fisheries had been over-fished, and three-fourths of the coral reefs were being eroded. This chapter profiles Apo Island, one of the oldest marine protected areas in the country; the scientific research on marine conservation and coastal resource management that led to its creation; and the challenges that the community has faced in maintaining its no-take zone. The chapter also describes the USAID-funded Coastal Resource Management Project and its work building local government capacity to manage coastal resources at a larger scale, using Malalag Bay, Mindanao, as an example.

This chapter analyzes the content and strategy of Darwin’s 1842 book, The Structure and Distribution of Coral Reefs. It was not the grand synthetic geological treatise he had originally envisioned writing, but it contained an elegant theory of reef formation supported by analysis of the structure and possible origin of every documented coral reef in the world. The first four chapters were ostensibly descriptive, but Darwin classified reefs into types that corresponded to developmental stages characterizing his theory, which emerged in chapter 5. The book concluded with extended discussion of the global distribution of different types of reefs, as illustrated and systematized on a fold-out thematic map (the only one of its sort Darwin ever published). Published reviews of the book emphasized (whether favorably or not) the ambitious scope of Darwin’s generalizing about reefs; he responded to some criticisms by heavily revising the chapter on coral reefs in a second (1845) edition of his Journal of Researches. Years hence he offered inconsistent and sometimes contradictory recollections about what he had accomplished with the book, reminding critics of his caution but privately reveling in the accuracy of his speculations when supporting evidence emerged from work by J.B. Jukes and J.D. Dana.

This chapter reveals the dazzling strategy underlying the content and presentation of Darwin’s 1837 Geological Society paper on the formation of coral reefs. While the paper might appear in retrospect to have been a mere precursor to Darwin’s 1842 book on the same topic, its arguments were distinct from earlier and later renditions of Darwin’s coral reef theory. This paper was remarkably ambitious: in it Darwin not only explained the formation of barrier reefs and atolls and argued that such reefs in turn were the key to interpreting the geological history of vast regions of the earth’s crust, he also forecasted that his new theory of reef formation might reveal the internal composition of the globe and explain the origin of species. The paper was also a sustained tribute to Lyell’s geological system. Nevertheless, attendees were shocked when Lyell responded by immediately disavowing his own published theory of reef formation in favor of Darwin’s new one. Sponsel demonstrates that Lyell and Darwin had planned this strategic retreat beforehand, and he argues that both men stood to benefit from Darwin’s emergence as a theoretical author who used Lyell’s general approach to supersede him on the topic of coral reefs.

In the last three decades of the twentieth century, scientists working in coral reef biology documented unprecedented and extensive changes and degradation of reefs worldwide. This chapter investigates the evolution of coral reef biology research during this critical period, focusing on the emergence and use in the field of an “infection repertoire” which as we document was borrowed from biomedical research. Coral reef biology researchers borrowed and used this repertoire, recognizing and leveraging critical institutional factors such as strategies to align their research with national and global funding priorities, as well as managerial decisions concerning the set-up, infrastructures, and technologies to be prioritized for the production and circulation of data. These institutional and managerial characteristics were as crucial to emerging approaches in the field of coral reef biology as were the conceptual and methodological factors relating to the identification and investigation of the causes of the changes being observed. The fruitfulness of the disease-related explanation of reef damage was not a serendipitous outcome of the application of a theoretical framework, but rather a well-engineered and deliberate choice made by a coalition of marine researchers who actively decided to reproduce a certain way of organizing and conducting research.

This chapter focuses on field studies to explore the role that predators play in nature. Based on practicing field ecologists, it suggests that such studies, although logistically more challenging, provide the best tools available for exploring the workings of nature. It also discusses laboratory studies that are particularly enlightening and provide insight not available from field studies. Much of the recent work on fish predation has been carried out on California's temperate reef fishes. To provide context and evaluate the generality of studies from California, the chapter compares this body of work to similar studies conducted elsewhere, mainly on tropical coral reefs. It concludes by highlighting several aspects of predation in particular that are in need of more detailed study.

This chapter explains how Darwin came to have a moment of insight about coral reef formation while at Tahiti in November 1835. Sponsel argues that this eureka moment depended on Darwin’s ability to envision the underwater realm like a hydrographer, a skill gained working alongside the Beagle’s maritime surveyors. Darwin’s Tahitian insight was also stimulated by his earlier conjecture that the floor of the Pacific Ocean was sinking, an idea derived too from Darwin’s experience with hydrography. Meanwhile, his physical surroundings as he climbed inland at Tahiti and gazed at the reef-encircled island of Eimeo [Moorea] also helped spark his new explanation of reef structures. Darwin’s resulting theory (in which corals grew upward on subsiding foundations to form ring-shaped reefs) echoed Humboldt’s description of the vertical zonation of vegetation on mountainsides, a phenomenon Darwin independently noted while climbing in Tahiti. The eureka moment shifted Darwin’s attention toward puzzles he had not previously addressed (such as atolls’ annular shape) and made a set of previous experiences seem as though they had always been intrinsically relevant to explaining reef formation. He began to pursue his new research not only in the field but by studying printed maps and books aboard the ship.

This chapter examines the two instances when Darwin had the opportunity to research coral reefs in the field, at the Cocos (Keeling) Islands in April 1836 and at Mauritius the following month. The visits offered very different circumstances for research and offer contrasting case studies of Darwin’s approach to field work. At the first location Robert FitzRoy and the Beagle’s other officers and crew carried out a hydrographic survey of South Keeling atoll; at Mauritius there was no surveying activity for Darwin to draw upon. Taken together these episodes show how much Darwin’s scientific work had come to depend on his shipmates’ expertise and labor. At South Keeling, Darwin was eager to determine whether the atoll’s deep structure favored his new subsidence-based theory over the prevailing view that atolls formed atop shallow submarine volcano craters. In addition to his natural history investigation of the living and fossil corals atop the reef and in shallow water he gained support for his theory from the surveyors’ deep soundings. At Mauritius, by contrast, Darwin had to conduct soundings himself, revealing that hydrographic practices were essential rather than supplemental to his research on reef structure and the distribution of corals.

Sound travels farther and faster in water than in air. Therefore, the introduction of artificial noise can interfere substantially with reproductive behaviors that include the production and reception of auditory signals. Sound production associated with reproductive behavior among marine fishes serves to synchronize the behavior of potential mates, thereby leading to successful fertilization. This chapter examines the role played by sound production and acoustic communication in the reproductive biology of many marine fish species. It summarizes findings concerning bioacoustics in shallow, tropical marine fishes (that is, coral reef fishes) and outlines the fish families known for sound production. The hope is that this status report will encourage further research in fish acoustic communication and underwater acoustic ecology. The evidence so far indicates that many coral reef fishes are most acoustically active during reproduction. It seems that some species produce sounds only when courting and mating, and not at all at other times.

This chapter opens part 1 of the book, “Theorizing on the Move,” by examining three major contexts or sources for Darwin’s ambition as a prospective naturalist. First, it describes the existence of a well-known and consequential scientific puzzle to which he would eventually offer a new answer: how were coral reefs formed? This question was of great practical significance to the British Admiralty and individual navigators, and it had important theoretical implications for geologists who were interested in the history of the earth. Second, the chapter explains the purpose of the 1831-1836 Royal Navy voyage of HMS Beagle and of Darwin’s presence aboard, emphasizing the role of Francis Beaufort in directing hydrographic surveyors to study coral reef formation in the South Seas. Third, it describes the range of intellectual and practical experiences Darwin brought to the voyage by examining his training at Edinburgh University and the University of Cambridge. This discussion calls attention to his expertise in the sciences of marine zoology and (terrestrial) geology, his early exposure to the work of Alexander von Humboldt, and the mentorship Darwin received from Robert Grant, John Stevens Henslow, and Adam Sedgwick.

This chapter summarizes the tool box of options for confronting the consequences of climate change through building local-scale adaptive capacity in societies and improving the condition of the natural resources on which people depend for their livelihoods. Building adaptive capacity will require strengthening appropriate aspects of a society’s flexibility, assets, learning and social organizations. The ways of doing this are diverse and will, of course, depend on existing local capacities and needs. Improving the condition of resources tends to require restricting or limiting society’s actions. For coral reef fisheries, options include restricting specific fishing grounds, the time that people can fish, the gear they can use, and the species they can capture. These two broad concepts, of building social capacities and limiting certain types of resource use, interact in complicated ways. Consequently, there is often a need for coupled actions that simultaneously govern resource use and build capacity in society.

This chapter reviews current knowledge about patterns in the distribution and diversity of marine fish species in the context of the enormous spatial and temporal variation that results from oceanographic variability. This chapter also discusses processes commonly implicated in controlling the distribution and regional diversity of marine fishes. Broader study of the genetics of putative species, especially widespread coral reef species and open-ocean species may reveal significantly greater cryptic species diversity. In addition, recent analysis indicates no decline in the rate of morphospecies descriptions of tropical shore-fishes in recent decades. The chapter is also couched within the prevailing concept of species. Broader application of a phylogenetic species concept, recently advocated for coral-reef fishes, would result in an increase in overall species diversity and a concomitant decrease in average species range.

This chapter considers the interchanges between mangrove and seagrass habitats and their immediate surroundings. Topics discussed include the distinctiveness of mangrove and seagrass communities, mangroves and salt marshes, interactions, outwelling, the fate of mangrove exports, larval dispersal and return, and commuting and other movement.