A central goal of coral-reef ecology is to define the key ecological processes that regulate reef populations under a rapidly changing environment. There is considerable need to move away from simply tracking reef state, and move toward more process orientated studies. Differential recruitment, growth, partial mortality, and mortality of corals are fundamental processes that need spatial evaluation using hierarchical sampling. Major changes to any one process will alter the state of the reef. Understanding these key processes, assessing their spatial variation and their relationship with state variables, such as coral cover, will lead to predictive models of population trajectories under different climate change scenarios. Predictions may even guide critical resource allocation to increase coral-reef management efforts at localities that are most likely to persevere in the prolonged struggle against unfavorable conditions.

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Natural history information is important for deciding the appropriateness of apparently proven theoretical models in particular cases, for interpreting controlled field experiments, for determining the ecological importance of individual species and the invasive potential of introduced species, for ground-truthing the extrinsic variables of ecological theory to evolutionary processes, for resolving unwarranted controversies into appropriate interpretations for different species, and for more effective and reliable management of resources. Manuscripts with natural history information are commonly devalued by reviewers of journals for functional and applied ecology, although they are still the foundation of journals for regional and evolutionary ecology. Gordon Orians concluded in 1962 that both functional ecology and evolutionary ecology are valid and useful, and it would be a mistake to construct ecological theory exclusively on either.

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Restoration of coastal reefs in the South China Sea started in the 1990s in response to widespread degradation of reef habitats. A wide variety of restoration techniques is practiced including coral transplantation, substrate modification, and non-coral species stock enhancement. Interesting lessons are derived from these experiences. Protection and management remains the foremost option and should continue to be strengthened. Restoration is more costly and has its limitations, but is at the same time regarded as necessary to address extensive reef loss. Much can be gained from the sharing of information and the combined experience will help to advance the science of reef restoration for the region.

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The present review summarizes the problems faced by reef building, zooxanthellate corals by the over two orders of magnitude in the underwater light field over their bathymetric range. The different levels by which corals optimize light harvesting and utilization are discussed on the molecular, biochemical, biophysical metabolic, behavioral and architectural levels. We show how the high energy striking shallow water reef tables is used, while avoiding its destructive photodynamic potential, and elucidate the means available to dim light, deep water coral colonies to survive on that meager resource.

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An important function of symbiont-bearing benthic foraminifera is to provide their endosymbiotic microalgae with light. At the same time, these foraminifera have to resist hydrodynamic forces. Foraminifera match these demands by constructing shells (tests) functioning as glasshouses. In shallowest regions of oligotrophic tropical seas, at the one end of the scale, foraminifera with spherical and thick lenticular tests develop special fixing mechanisms to resist extreme water motion. In the deepest euphotic zone, at the other end of the scale with extremely weak light and quiet water, foraminifera with flat discoid and blade-shaped tests possessing a high surface/volume-ratio position their symbionts just beneath the transparent test walls, intensifying the weak light through elevated test surface structures. Between these two extremes, foraminifera react to decreasing light intensity and water motion by the transition in shell form from spherical to extremely flat tests. A second way in test form from high energetic shallow water to less, but still energetic water is the transition from spherical to fusiform tests, again raising the surface/volume-ratio but not in the same degree as performed by test flattening.

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Spatial analyses of coral distributions at species level delineate the Coral Triangle and provide new insights into patterns of diversity and endemism around the globe. This study shows that the Coral Triangle, an area extending from the Philippines to the Solomon Islands, has 605 zooxanthellate corals including 15 regional endemics. This amounts to 76% of the world's total species complement, giving this province the world's highest conservation priority. Within the Coral Triangle, highest richness resides in the Bird's Head Peninsula of Indonesian Papua which hosts 574 species, with individual reefs supporting up to 280 species ha^-1. Reasons for the exceptional richness of the Coral Triangle include the geological setting, physical environment and an array of ecological processes. These findings, supported by parallel distributions of reef fishes and other taxa, provide a clear scientific justification for the Coral Triangle Initiative, arguably one of the world's most significant reef conservation undertakings.

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The annual mass spawning of scleractinian corals on the Great Barrier Reef (GBR), Australia, is purported to be unprecedented in terms of the taxonomic and geographical scale of spawning synchrony. Here, we compare spawning synchrony both within and among coral species in four regions spanning 10°of latitude on the GBR and compare this with four regions separated by a similar latitudinal range within the Japanese tropical and sub-tropical Archipelago. On the GBR, peak reproductive activity at all latitudes occurred in November whereas there was a clear disjunction in the period of peak reproductive activity among the four regions in Japan, with tropical locations spawning up to 3 months earlier. In Sekesei Lagoon (22°N), a high proportion of Acropora colonies were mature following the full moon in April; at Akajima Island (26°N) peak reproductive activity occurred in May; at Oku (28°N) peak reproductive activity occurred in June and in Amakusa (31°N), reproductive activity likely peaked in July. However, mature colonies of Acropora were found prior to every full moon for at least 5 months at two regions examined in detail (The Whitsundays Islands on the GBR and Akajima Island). While these regions on GBR appear to act more homogeneously than regions over a similar latitudinal range in Japan with respect to the timing of peak reproductive activity, and the proportion of colonies mature was often higher during these peaks, the reproductive season on the GBR is much longer (5 months) than is typically appreciated.

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The coral Galaxea fascicularis exhibits marked variation in polyp color and several color morphs have been described (e.g. brown polyp with green oral disc, BG; brown with green septal tentacles, Gs; brown with white fluorescent tentacles, Wt). Color morphs of sessile marine invertebrate species may exhibit considerable differences in their capacity to absorb UV radiation, although only a few studies have examined intra-species variation in the UV-absorbing compounds, mycosporine-like amino acids (MAAs). The objective of this study was to investigate possible differences in the composition and quantity of MAAs in the coral tissue and symbiotic algae of several G. fascicularis color morphs. Marked differences in the composition and quantity of MAAs were found between the BG and Gs/Wt morphs of G. fascicularis, both in the coral tissue and freshly isolated symbiotic algae. Future studies, especially genetic analyses of corals and their symbionts, are necessary to understand whether these observed differences in the composition and quantity of MAAs reflect phylogenetic or biogeographical differences among the corals.

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The reproductive modes of corals in the family Fungiidae are relatively poorly known. In this study we document the findings over five years of observations of various reproductive traits and seasonal reproductive patterns of 12 species of mushroom corals from northern Okinawa. We provide new records with respect to sexuality and mode of reproduction for six species: Ctenactis crassa, Fungia paumotensis, F. scruposa, F. granulosa, Halomitra pileus and Sandalolitha dentata. Furthermore, we indicate two new species that change sex (C. crassa and F. scruposa), as well as identify F. fungites in Okinawa as a gonochoric brooder. We estimate the reproductive effort of C. echinata, C. crassa and F. repanda for the months of July and August of the years 2007-2009, discuss their diurnal rhythms, degree of spawning overlap and the potential for hybridization vs. temporal reproductive isolation in these species. We conclude by highlighting the fungiids as ideal model organisms for studies of reproductive ecology, larval development and the evolution of life-history traits.

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We observed a severe reduction in salinity around Khang Khao Island at the end of the rainy season in September and October, 1995, caused by the most serious freshwater flooding in Thailand in recent 15 years. During low tide, corals around Khang Khao Island were exposed to 23‰ at three meters depth, and 25‰ at five meters. As a result, Pocillopora damicornis and a few species of Acropora showed colony bleaching or partial or complete colony death in the field. On the other hand, Porites spp., the dominant corals of this area, did not show any conspicuous effects. Porites lutea could survive five days of experimental exposure to 17‰, the critical salinity for other corals. The chlorophyll-a concentration of P. lutea that become partially bleached after seven days exposure to 20‰ was higher than in normal control fragments. These phenomena suggest that P. lutea has a compensation mechanism against salinity reduction. Both field observations and experiments suggest that lowered salinity caused by runoff during the rainy season is an important factor besides turbidity in establishing the characteristics of the coral community structure around Khang Khao Island. A detailed study of the process of coral community formation in this area may contribute to an understanding of not only the negative effects of continental great rivers on the establishment of coral reefs around tropical continental shores but also the influence of the heavy rainfall on a coral community in the coral reef region by the global climate change.

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The illuminated parts of many hermatypic corals have higher levels of photosynthetic pigments and symbiotic dinoflagellates belonging to the genus Symbiodinium than the shaded parts that often appear pale. In the field, we observed that the perforate coral Montipora capitata restored this original pattern after being overturned by disturbance. Here, two hypotheses were tested to account for this phenomenon, using experimentally overturned M. capitata plates in the laboratory. Our results indicated that restoration of the original pattern was not due to changes in chlorophyll a content per Symbiodinium cell or alterations in symbiont density through differential division rates. Instead, Symbiodinium cells appear to be translocated within the colony. This finding demonstrates an additional photoacclimatory process for hermatypic corals, whereby new Symbiodinium cells proliferate in shaded parts of the colony where they are protected from potentially high levels of solar irradiance and are then transported to illuminated parts of the colony (and possibly released from the colony when damaged). Additional studies in other species are required to determine if this dynamic spatial and temporal process is a general property of the hermatypic coral-Symbiodinium relationship.

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On the shallow sandy bottom in the innermost part of the Gulf of Thailand, the regular sea urchin Salmacis sphaeroides feeds on two spatangoid urchins: Brissus latecarinatus, one of the locally dominant infaunal macrobenthic animals, and Lovenia elongata. Aggregations of Salmacis were frequently seen on the soft bottom during a survey of the macrobenthos in the Gulf, and Brissus individuals lacking spines were found beneath the aggregations. Brissus species, which are infaunal, were attacked by Salmacis, although the reason for their presence on top of the sandy bottom remains unknown. Salmacis were seen feeding first on the spines of Brissus, exposing the test. Occasionally, Salmacis carrying empty, broken tests of Brissus were observed, indicating that the Brissus organs were also eaten by Salmacis. The fact that Salmacis ate several kinds of food items such as water hyacinths originated from the nearby river system, sea pens, jellyfish, and other urchins indicates that this species is an omnivore. Cannibalism was also found both in the field and laboratory. The feeding strategy of Salmacis has evolved to incorporate diverse food items, but Brissus is undoubtedly an important food source because of its high abundance.

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The soft coral Scleronephthya gracillimum (Alcyonacea: Octocorallia), a member of family Nephtheidae, is abundant in the southern part of Jejudo Island, Korea. To examine the sexual reproductive pattern, monthly collections and histological studies were conducted from June 2003 to October 2007. The sexual reproductive pattern of the genus Scleronephthya was described for the first time in the present study, which established that S. gracillimum is a gonochoric broadcaster, with the sex ratio of 1:1. The gametogenic cycle was annual, and a difference between female and male colonies was apparent, with biorhythms of 12 and 5-7 months respectively. Gametogenesis and spawning are related to seasonal factors such as seawater temperature and algal blooms. Actual spawning event occurred, and others may have taken place, when seawater temperature attained an annual peak between August and September. The actual spawning occurred in the field at 10 a.m. on September 3, 2006, 4 days before the full moon.

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Carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N) of organic matter of five species of reef building corals from Sesoko Island (Okinawa, Japan) and Mun Island (Nhatrang, Vietnam) and monodominant community of the endolithic alga Ostreobium quekettii inhabiting live and dead portions of these coral colonies were determined. There were no significant interand intraspecific differences in the isotope composition of soft tissues of tested corals as well as differences among corals containing and non-containing endolithic algae. Corals showed mean values of δ¹³C and δ¹⁵N −14.3±1.3‰ and 5.3±0.6‰, accordingly. Endolithic algae living in the neighborhood with coral polyps showed similar carbon and nitrogen isotope values (δ¹³C=−16.0±3.3‰, δ¹⁵N=5.1±0.6‰). At the same time, carbon of endolithic algae inhabiting dead portions of coral colonies was heavier approximately by 3.2‰ than carbon of endolithic algae inhabiting live corals while nitrogen was significantly lighter by 1.4‰. The similarity in carbon and nitrogen isotope values between coral polyps and endolithic algae may be attributed to a common source of these elements for zooxanthellae and endolithic algae, namely from respiration and metabolism of nitrogen by the coral host accordingly.

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A total of 87 beach rock samples were collected from 37 sites of Amami Islands in order to determine formative ages of beach rocks on Amami Islands, and to clarify the sea-level change during the late Holocene period. Beach rocks began to form 5,720 yrs cal BP on Yoron Island at first, and formed continuously between 4,050 yrs cal BP and 380 yrs cal BP on the sandy coasts of Amami Islands. Relative sea-levels during the late Holocene period on Yoron Island and Okinoerabu Island were slightly higher than those of the present sea-level. Geomorphic evidences indicate that the islands have probably uplifted by earthquakes occurred along the subduction zone of Eurasian Plate. However the sea-level has remained similar to the present since at least the past 4,000 years at Amami-Oshima Island.

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Species richness of asteroids, echinoids, and holothuroids was surveyed on shallow reefs at 6 sites across the tropical west Pacific: Seto, on the west coast of the Kii Peninsula, Honshu Island; Okinawa, Ryukyus Islands; Madang, Papua New Guinea; Palm Islands, Queensland, Australia; ‘Upolu, Western Samoa; and Moorea, French Polynesia. A total of 113 nominal species were recorded. No species was unambiguously found at all 6 sites, only 17 (15%) were found at 4 or more sites, and 63 (56%) were found at only one site. Single-site finds represented 48% of the species at Seto, 21-32% of the species at 4 other sites, and only 4% (1 species) at ‘Upolu. Madang had the most species (74), followed by Okinawa (54), Moorea (34), Samoa (25), Seto (23), and the Palm Islands (15). Although Seto had a diverse echinoid fauna (17 species), including several temperate forms, there was a dearth of asteroids (4) and holothuroids (2). In contrast, all 3 classes were well represented on the reefs of Okinawa (11 asteroids, 16 echinoids, and 27 holothuroids) and Madang (22 asteroids, 17 echinoids, 35 holothuroids), both of which had a rich diversity of widespread tropical oceanic species. Substantially fewer species were found farther to the east, at Samoa and Moorea, consistent with the pattern seen in other taxa. Species richness was surprisingly low around the Palm Islands on the inner portion of the Great Barrier Reef, perhaps because of human disturbance causing run-off from the land and siltation.

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We investigated the mollusk fauna of 53 closed lagoons (atolls without passes) among the 83 French Polynesian atolls. These confined lagoons of closed atolls reveal a limited diversity of mollusks but with wide distribution of some species. A few species occur in these lagoons but each lagoon is unique with a particular qualitative mollusk composition related to only 5 species: Tridacna maxima, Pinctada margaritifera, Pinctada maculata, Chama iostoma and Arca ventricosa. Due to the absence or poor data on 14 closed lagoons, our detailed study was limited to 39. We characterised the mollusk fauna of each closed lagoon and attempted to identify group of lagoons with the same dominant mollusk composition. T. maxima, the giant clam, appeared to be the most characteristic species of these confined lagoons with large densities and populations in 32 of the 39 lagoons. P. margaritifera, the mother-of-pearl oyster, also occurs as large populations in 18 lagoons; these two species are of economic importance now as they were in the past. The three other species mentioned above occurred respectively in 25, 28 and 20 lagoons. There are 11 lagoons with original and unique characteristics (their assemblages of dominant species do not occur in any other lagoon), 28 are grouped in 7 categories of assemblages. The most numerous groups contain all 5 species or at least 4 of them. Research topics are suggested in order to understand the ability of each mollusk species to colonize and maintain its dominance in a confined lagoon.

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This paper documents the conditions of selected coral communities in the Gulf of Thailand with an insight into the degree of resistance and resilience to coral bleaching and localized anthropogenic disturbances. Live coral coverage at the study sites ranged from 5.2% at Koh Samui to 64.3% at Koh Lan. The most dominant coral species was Porites lutea. Only a few colonies of Acropora were found at the study sites. The most abundant macrobenthic animal was the sea urchin, Diadema setosum, with the highest population density 7.9 of individuals/m² at Koh Khang Khao and D. setosum was not recorded in the belt transects at Koh Samui. Most coral colonies at Koh Lan showed partial mortality (77%), mainly pink spot and white band syndromes, and reflected potential impacts from coastal tourism. The highest recorded juvenile coral density was 8.3 colonies/m² at Koh Kood while the lowest one was 1.1 colonies/m² at Koh Khang Khao. The most abundant juvenile coral at all study sites was Porites spp. The occurrence of low live coral coverage and juvenile coral density in conjunction with high densities of the sea urchin D. setosum at Koh Khang Khao may partly explain why there are no structural reefs on the coasts of many islands in the inner part of the Gulf of Thailand. In addition, the present study documents macroalgae-dominated communities at Koh Samui and implies appropriate strategies and measures for coral reef restoration.

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Manado Bay fronts Manado City, North Sulawesi with its total population of ca. 500,000 people. In 1992, the governmetn established a National Park in the bay to protect coral reef ecosystems on five particular islands facing Manado Bay. Life Form Category by Linear Intercept Transect in 2 sites has good conditions (ca. 55%), 2 sites have moderate (ca. 30%), and the other 2 (two) sites are in a poor condition (<20%). In comparison to studies from the early 1990s the present coral condition seems to have decreased. Anthropogenic activities from the city and the increasing number of foreign and domestic visitors who dive in the park are probably the cause of the park's coral deterioration in Manado Bay. Since 1996, new construction and coastal reclamation in the city have also used the hard substrates for new coral recruitment. However, the excellent grade of water quality in the bay is an important factor in which the new coral colonies have successfully settled on the new hard substrate.

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