Coral reef cryptofauna (coelobites) are metazoans that occupy the hidden recesses formed by structural taxa such as corals. While cryptic communities are thought to account for the majority of reef biodiversity and play important roles in reef trophodynamics, little empirical evidence exists supporting these claims. Quantitative sampling of coelobites has been thus far limited due to highly heterogeneous reef topographies as well as difficulties associated with identification of large numbers of species. In the eastern Pacific, monogeneric stands of Pocillopora form reef structures that are homogeneous across a horizontal plane and support a relatively depauperate fauna, thereby permitting detailed multispecies analysis. Sampling of motile cryptofauna associated with live coral and dead coral frameworks typifying four levels of degradation, was conducted at Playa Larga Reef on Contadora Island in the eastern Pacific, Gulf of Panamá. Communities associated with live coral colonies were less diverse than those associated with dead corals and the species richness of cryptofauna living on dead coral substrates was higher in more degraded habitats. Living coral colonies, however, support significantly greater densities of cryptofauna and more biomass per volume substrate than their dead coral counterparts. On dead coral frameworks, numbers of individuals and biomass were significantly greater per volume in areas of intermediate degradation. A field experiment was conducted to test the effects of flow, porosity and coral cover on cryptic communities associated with artificial reef frameworks (ARFs). Coral cover (live vs. dead) was not observed to affect the structure of communities occupying underlying frameworks, however, lower porosity substrates sheltered greater abundances of individuals per volume substrate and low flow environments supported elevated biomass. Additionally, porosity and flow were both found to significantly affect relative species abundances as well as overall community diversity. Data from quantitative sampling of natural reef environments and experimental manipulation of cryptic reef habitats suggest novel and unexplored responses to mass coral mortality and reef habitat degradation. Coral death is considered to be vital to the maintenance of reef ecosystem habitat and biotic diversity. Contrary to the popular paradigm that a healthy reef ecosystem has high coral cover, the most diverse reef ecosystems are those which have experienced intermediate levels of degradation. Furthermore, while living corals support elevated cryptofauna abundances and biomass, the magnitude of communities associated with dead framework materials suggest that abundant cryptofauna populations persist in highly degraded reef environments.

Modeling of wave energy transformation and breaking on fringing reefs is inherently difficult due to the unique topography of reefs. Prior methods of determining dissipation are based on empirical data from gently sloping beaches and offer only bulk energy dissipation estimates over the entire spectrum. Methods for deducing a frequency-dependent dissipation have been limited to hypothesized linkages between dissipation and wave shape in the surf zone, and have used bulk dissipation models as a constraint on the overall dissipation for mild sloping beaches. However, there is no clear indication that the constraint on the overall level of dissipation is suitable for the entire reef structure. Using these constraints the frequency-dependent dissipation rate can be deduced from laboratory data of wave transformation over reefs, taken at the Coastal and Hydraulics Laboratory. The frequency-dependent dissipation rate can then be integrated over the spectrum to derive an empirically-based counterpart to energy flux dissipation. Comparing the bulk energy dissipation estimates for the reef system to the frequency based method allows for the modification of wave breaking parameters in the frequency based estimation. Since this method is based on the Fourier transform of the time series data, it allows the dissipation to be found as a function of the frequency. This analysis shows that there is a correlation between the amount of energy in the low frequencies of the wave spectrum and certain characteristics of the frequency-dependent dissipation coefficient.

During the last three decades of coral reefs studies, the large areal coverage of data derived from satellite images has increasingly been used to complement the more detailed but spatially limited data produced by conventional fieldwork. Continuous improvement in sensor capabilities, along with the development of increasingly refined methods for image processing, has lead to ever more accurate maps of physical and biological variables of importance to reef ecology. During the same period, an abundance of field studies have documented statistical relationships between aspects of the reef habitat and its fish community. Despite numerous stochastic influences, such as spatially concentrated and temporally variable fish recruitment pulses or the selective and patchy mortality caused by fishing, several aspects of habitat have been shown to significantly influence the fish community. Fortunately the most important of these, water depth, the structural complexity of the reef, and the cover of live coral, are possible to estimate from currently available satellite imagery. The research presented in the following pages has combined the statistical relationships between the fish community and its habitat with the capability of satellite imagery to map that habitat, thereby answering the research question: How can remote sensing be used to map coral reef fish communities? In the process, a set of new techniques for predictive modeling of complex relationships have been compared, the influence of a range of habitat variables on the fish community quantified, the spatial scales at which the fish-habitat relationships are strongest have been explored, and new methods for deriving estimates of some aspects of the coral reef habitat from satellite imagery have been developed. The results presented in this thesis thus contribute to the further understanding of fish-habitat relationships, while providing a template for producing spatially explicit predictive models of fish community variables. This is not only of scientific interest, but also of substantial value to the conservation community that tries to protect the world’s remaining healthy coral reef ecosystems, and their fish communities, from an array of man-made influences.

During the last three decades of coral reefs studies, the large areal coverage of data derived from satellite images has increasingly been used to complement the more detailed but spatially limited data produced by conventional fieldwork. Continuous improvement in sensor capabilities, along with the development of increasingly refined methods for image processing, has lead to ever more accurate maps of physical and biological variables of importance to reef ecology. During the same period, an abundance of field studies have documented statistical relationships between aspects of the reef habitat and its fish community. Despite numerous stochastic influences, such as spatially concentrated and temporally variable fish recruitment pulses or the selective and patchy mortality caused by fishing, several aspects of habitat have been shown to significantly influence the fish community. Fortunately the most important of these, water depth, the structural complexity of the reef, and the cover of live coral, are possible to estimate from currently available satellite imagery. The research presented in the following pages has combined the statistical relationships between the fish community and its habitat with the capability of satellite imagery to map that habitat, thereby answering the research question: How can remote sensing be used to map coral reef fish communities? In the process, a set of new techniques for predictive modeling of complex relationships have been compared, the influence of a range of habitat variables on the fish community quantified, the spatial scales at which the fish-habitat relationships are strongest have been explored, and new methods for deriving estimates of some aspects of the coral reef habitat from satellite imagery have been developed. The results presented in this thesis thus contribute to the further understanding of fish-habitat relationships, while providing a template for producing spatially explicit predictive models of fish community variables. This is not only of scientific interest, but also of substantial value to the conservation community that tries to protect the world’s remaining healthy coral reef ecosystems, and their fish communities, from an array of man-made influences.

Coral reefs have high biodiversity among the many marine ecosystems. Many hypotheses explain marine biodiversity, e.g., the Intermediate Disturbance Hypothesis, the Lottery hypothesis and the Resource Allocation Hypothesis, but there is no mention of the possible role of seasonal effects. Here, we propose the Seasonal Recruitment Hypothesis to explain the possible role of seasonal recruitment and succession in a disturbed ecosystem. In this investigation, we tested several prediction of the hypothesis: a. Does recruitment have seasonal variation? b. Does variable recruiting communities diverge in succession? c. Are high biodiversities of coral reefs contributed by different communities originating from patches created in different seasons? In this study, we used plastic plates as proxy of empty space generated after disturbance to survey the seasonal patterns of settling benthos. Recruitment plates were placed and retrieved at two-month intervals for two consecutive years. Then, the composition and densities of settled taxa were estimated. The PRIMER software was used to compare the community similarities. We looked for possible seasonal patterns in each benthic populations but found few not real examples of such. Although there is difference between communities started in different seasons, no cyclic pattern in similarity was found by MDS plots in two years of recruitment communities. There are variations of recruitment community between different year and month, and the community structures converged after succession. These results do not support the prediction of the Seasoanl Recruitment Hypothesis.

Terpios hoshinota is coral-killing sponge which grows and covers most stony corals in shallow waters. It was first discovered at Green Island in 2006, and have since killed a lot of coral, yet we know little about the physiology of Terpios hoshinota. This research focuses on the propagation and growth of the sponge. In the sexual reproduction part, we collected tissue samples in 2009 and 2010, the sperm cells were found only in Jun and Aug in 2009. The oocytes were found in Apr, Jul, and Aug. In 2010, embryos occurred. No lunar pattern was found in a high-frequency sampling of tissues comparing the occurrence and sizes of oocytes and embryos. Embryos are more likely to be found in the central part of the sponge; this pattern does not apply to oocytes nor to sperm cells. The sponge may be hermaphroditic male and female gametes are developed at different locations or times. The sponge fragments can reinfect new host corals, although such capability decreased with increasing number of days suspending in the water column. The spicules parallel to each other and to the growth axis in tissue threads, moreover, the sponge quickly extended numerous tissue threads in the absence of adequate coral substrate, which may serve the function of reaching new hosts. The sponge grows faster under light than under dimmed conditions. Fusion of tissues could occur between non-identical genotypes, and allografting pairs of tissues have higher rates of rejection than isografting pairs. After allografting the sponge fragments from different areas, the fusion rates were depended on the distance of two populations in the northern coast of Green Island. The results supported that self-seeding is the mechanism how Terpios hoshinota populations exploded in the north coast Green Island. The ability to cross to the neighboring corals, to propagate by fragments, and to produce embryos may have all contributed to their self-seeding capability.

Terpios hoshinota is a blackish-gray cyanobacteriosponge encrusting on stony corals with fast expansion rates in shallow waters. The sponge population exploded at Green Island and Orchid Island during 2006 to 2008. Here, we surveyed at Green Island and Orchid Island in 2009 and 2010, compared the sponge densities, individual lengths, sponge coverage and scleractinian coral coverage between 2008 and 2010. We also tested the hypothesis that typhoon may play a role inhibiting the sponges by monitoring individual sponges before and after. In these three years, the sponge coverages remained the same; sponge length and densities had no significant difference at 2~3 m depth at Green Island, but densities decreased and length increase at 5 m depth at Green Island and 2~3 m depth at Orchid Island, but the rate increased was significant slower than average growth speed . Although sponge coverages were not significant different between these years, the scleractinian corals coverages decreased at Green Island among these years. The main wind direction was southwest during the Typhoon Marakot at Green Island, and only the sponges at southwest coast of Green Island decreased in size significantly among the three coasts monitored. The population of Sponge T. hoshinota exploded in 2006, the strength of typhoons were smaller than other years during 2005 to 2009. The typhoon may be the main factor that inhibiting the sponge T. hoshinota at these two islands.

Benthic community structure was studied by sample quadrates on transects at depths of 5 to 10 m in four sites, including Wanlitong, Leidashih, Siangjiao Bay, and Longkun, in coral reefs of southern Taiwan from 2003 to 2005. Totally 154 species in 45 genera of hard coral and 45 species in 10 genera of soft coral, representing 67% of known coral species were recorded. Covers of benthic organisms and hard coral growth forms were similar among years, but were significantly different among sites. Mean cover of all corals was high in Siangjiao Bay (56.88%) and Leidashih (65.69%), but hard coral (65.43%) was dominanted in Siangjiao Bay while soft coral (39.00%) was dominanted in Leidashih. Mean cover of all coral and benthic algae was similar in Wanlitong and Longkun. For hard coral growth forms, massive and encrusting corals were dominanted in three of four sites. This may be resulted from the strong wave. Cover of bare substrate was high (21.39%) in Longkun which was the most exposed to wind and wave stress. Foliaceous coral was abundant with the dominated species, Montipora aequituberculata (20.59%) in Siangjiao Bay which was a more protected site. However, foliaceous coral was more susceptibe to typhoon. Coral diversity was higher in Leidashih. This was related to both hard and soft corals were common and no dominant species. Comparing to previous studies, the long term change of coral abundance shows stable and/or increasing trends. It may be related to the dominance of massive and encrusting coral communities in southern Taiwan.

Sea levels fluctuated following glacial cycles during the Pleistocene, reaching approximately 115-130m below current sea levels in the Indian and Pacific Oceans during the last glacial maximum 17,000 years before present. The effects of these sea level fluctuations on population structure have been shown in many near-shore marine taxa, revealing several common patterns. However, the underlying mechanisms behind these observed patterns are largely unknown. Drops in sea level affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes where shelf breaks are shallow. In these circumstances, we expect that species inhabiting lagoons should show reduced genetic diversity relative to species inhabiting more stable outer reefs. Here, I tested this expectation on the scale of an entire ocean-basin with four wrasses (genus Halichoeres): H. claudia (N=194, with ocean-wide distribution) and H. ornatissimus (N=346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N=239) and H. margaritaceus (N= 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations and a historically stable population. Mismatch distributions and significant negative Fu’s F values indicate Pleistocene population expansion for all species, and (contrary to expectations) reduced genetic diversity in the outer slope species. These data indicate that lagoonal species may persist through the loss of habitat, but are restricted to isolated refugia during lower sea level stands, which may inflate genetic diversity during high sea levels. Outer reef slope species on the other hand have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles. / text

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