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Reef-building corals are found across > 30° of latitude from tropical to temperate regions, where they occupy habitats greatly differing in seawater temperature and light regimes. It remains largely unknown, however, how the demography of corals differs across this gradient of environmental conditions. Variation in coral growth is especially important to coral populations, because aspects of coral demography are dependent on colony size, with both fecundity and survivorship increasing with larger colonies. Here we tested for latitudinal variation in annual growth rate and survival of juvenile corals, using 11 study locations extending from 17° S to 33° N in the West and South Pacific. Regression analyses revealed a significant decline in annual growth rates with increasing latitude, whereas no significant latitudinal pattern was detected in annual survival. Seawater temperature showed a significant and positive association with annual growth rates. Growth rates varied among the four common genera, allowing them to be ranked Acropora > Pocillopora > Porites > Dipsastraea. Acropora and Pocillopora showed more variation in growth rates across latitudes than Porites and Dipsastraea. Although the present data have limitations with regard to difference in depths, survey periods, and replication among locations, they provide evidence that a higher capacity for growth of individual colonies may facilitate population growth, and hence population recovery following disturbances, at lower latitudes. These trends are likely to be best developed in Acropora and Pocillopora, which have high rates of colony growth.

To evaluate potential coral adaptive mechanisms, we investigated physiological traits (biomass, lipid, protein, chlorophyll, and isotopic proxies for trophic strategy) in eight Hawaiian corals species along an environmental gradient of significant wave height, sea surface temperature, and seawater chlorophyll a concentration around the island of O‘ahu, Hawai‘i. We used the amount of physiological variation expressed in corals, and the proportion of this variation that could be explained by environmental variables, to construct hypotheses about the relative capacity for each species to adapt or acclimatize to differing conditions. Genus-level analyses indicated that Montipora and Pocillopora phenotypes are influenced more strongly by the environment than Porites corals. Species-level analyses revealed that Montipora capitata and Pocillopora acuta have the widest physiological niche boundaries, whereas Porites evermanni and Pocillopora meandrina are more physiologically restricted. Correlations between individual traits and the environmental gradient provided insight into potential adaptive mechanisms employed by each species that allow them to persist in reefs such as those within Kāne’ohe Bay, where water flow is lowest, and temperature, acidity, and nutrient concentrations are highest relative to other reefs around O‘ahu. Potential adaptive mechanisms included (a) increased surface-area-to-volume ratios to facilitate higher material flux across the diffusive boundary layer and/or to maximize light harvesting (M. capitata and P. acuta), (b) strategic investment of metabolic energy toward energy reserves (Montipora and Pocillopora), (c) changes in protein management likely via differential expression and function (Porites), and d) increased chlorophyll concentration per Symbiodiniaceae cell to maximize photosynthesis (Porites compressa). Comparison of our results with established patterns in the relative abundance of these species around O‘ahu suggests that species with wide physiological niche boundaries like M. capitata and M. flabellata might be expected to do better under predicted future ocean conditions and outcompete species such as P. evermanni and P. meandrina, making them potential candidates for coral conservation efforts.

Global- and local-scale anthropogenic stressors have been the main drivers of coral reef decline, causing shifts in coral reef community composition and ecosystem functioning. Excess nutrient enrichment can make corals more vulnerable to ocean warming by suppressing calcification and reducing photosynthetic performance. However, in some environments, corals can exhibit higher growth rates and thermal performance in response to nutrient enrichment. In this study, we measured how chronic nutrient enrichment at low concentrations affected coral physiology, including endosymbiont and coral host response variables, and holobiont metabolic responses of Pocillopora spp. colonies in Mo'orea, French Polynesia. We experimentally enriched corals with dissolved inorganic nitrogen and phosphate for 15 months on an oligotrophic fore reef in Mo'orea. We first characterized symbiont and coral physiological traits due to enrichment and then used thermal performance curves to quantify the relationship between metabolic rates and temperature for experimentally enriched and control coral colonies. We found that endosymbiont densities and total tissue biomass were 54% and 22% higher in nutrient-enriched corals, respectively, relative to controls. Algal endosymbiont nitrogen content cell−1 was 44% lower in enriched corals relative to the control colonies. In addition, thermal performance metrics indicated that the maximal rate of performance for gross photosynthesis was 29% higher and the rate of oxygen evolution at a reference temperature (26.8 °C) for gross photosynthesis was 33% higher in enriched colonies compared to the control colonies. These differences were not attributed to symbiont community composition between corals in different treatments, as C42, a symbiont type in the Cladocopium genus, was the dominant endosymbiont type found in all corals. Together, our results show that in an oligotrophic fore reef environment, nutrient enrichment can cause changes in coral endosymbiont physiology that increase the performance of the coral holobiont.

Cryptic species that are morphologically similar co-occur because either the rate of competitive exclusion is very slow, or because they are not, in fact, ecologically similar. The processes that maintain cryptic local diversity may, therefore, be particularly subtle and difficult to identify. Here, we uncover differences among several cryptic species in their relative abundance across a depth gradient within a dominant and ecologically important genus of hard coral, Pocillopora. From extensive sampling unbiased toward morphological characters, at multiple depths on the fore reef around the island of Mo’orea, French Polynesia, we genetically identified 673 colonies in the Pocillopora species complex. We identified 14 mitochondrial Open Reading Frame haplotypes (mtORFs, a well-studied and informative species marker used for pocilloporids), which included at least six nominal species, and uncovered differences among haplotypes in their relative abundance at 5, 10, and 20 m at four sites around the island. Differences in relative haplotype abundance across depths were greater than differences among sites separated by several kilometers. The four most abundant species are often visibly indistinguishable at the gross colony level, yet they exhibited stark differences in their associations with light irradiance and daily water temperature variance. The pattern of community composition was associated with frequent cooling in deeper versus shallower water more than warmer temperatures in shallow water. Our results indicate that these cryptic species are not all ecologically similar. The differential abundance of Pocillopora cryptic species across depth should promote their coexistence at the reef scale, as well as promote resilience through response diversity.

Anthropocene coral reefs are faced with increasingly severe marine heatwaves and mass coral bleaching mortality events. The ensuing demographic changes to coral assemblages can have long-term impacts on reef community organisation. Thus, understanding the dynamics of subtropical scleractinian coral populations is essential to predict their recovery or extinction post-disturbance. Here we present a 10-yr demographic assessment of a subtropical endemic coral, Pocillopora aliciae (Schmidt-Roach et al. in Zootaxa 3626:576–582, 2013) from the Solitary Islands Marine Park, eastern Australia, paired with long-term temperature records. These coral populations are regularly affected by storms, undergo seasonal thermal variability, and are increasingly impacted by severe marine heatwaves. We examined the demographic processes governing the persistence of these populations using inference from size-frequency distributions based on log-transformed planar area measurements of 7196 coral colonies. Specifically, the size-frequency distribution mean, coefficient of variation, skewness, kurtosis, and coral density were applied to describe population dynamics. Generalised Linear Mixed Effects Models were used to determine temporal trends and test demographic responses to heat stress. Temporal variation in size-frequency distributions revealed various population processes, from recruitment pulses and cohort growth, to bleaching impacts and temperature dependencies. Sporadic recruitment pulses likely support population persistence, illustrated in 2010 by strong positively skewed size-frequency distributions and the highest density of juvenile corals measured during the study. Increasing mean colony size over the following 6 yr indicates further cohort growth of these recruits. Severe heat stress in 2016 resulted in mass bleaching mortality and a 51% decline in coral density. Moderate heat stress in the following years was associated with suppressed P. aliciae recruitment and a lack of early recovery, marked by an exponential decrease of juvenile density (i.e. recruitment) with increasing heat stress. Here, population reliance on sporadic recruitment and susceptibility to heat stress underpin the vulnerability of subtropical coral assemblages to climate change.

Length–weight relationships (LWRs) are a fundamental tool for the non-intrusive determination of biomass, a unit of measure that facilitates the quantification of ecosystem and fisheries productivity. LWRs have been defined and broadly applied for many marine species across a range of ecosystems, especially regarding fishes. However, LWRs are yet to be determined for the majority of marine taxa, particularly for small cryptic organisms that are difficult to census and poorly described. On coral reefs, the motile cryptofauna represent the greatest density and diversity of metazoan taxa that likely support critical steps in trophic pathways, but little empirical data exist beyond biodiversity assessments. We evaluated LWRs for 42 groups of motile cryptofauna across four microhabitats (live Acropora, live Pocillopora, dead branching coral and coral rubble) in Palau, Western Micronesia. We employed a robust methodology to determine LWRs by comparing the suitability of a series of linear, quadratic, polynomial and power models. Using the best-fit equations for each group, we provide the first documented LWRs for motile cryptofauna, namely at the level of family. LWRs were well fit (R2 > 0.90) for 45% of the groups and reasonable (R2 > 0.70) for 76%. The presence, size and weight of cryptofauna varied among microhabitats with the size distribution of 13 groups significantly influenced by habitat type. Establishment of these LWRs provides critical baseline information regarding an overlooked group on coral reefs, making population data on the cryptofauna more accessible to support future research aiming to characterise the roles of these taxa in ecosystem functioning and trophodynamics.

Coral ecosystems in the central Mexican Pacific inhabit environmental conditions considered as suboptimal for reef development, such as wide ranges in temperature, low pH, and cyclonic activity. In addition, they are facing increasing nutrient and sediment inputs as a consequence of urban growth and tourism. While the global effects of anthropogenic stressors to coral communities have been described, the local response and microscale variations remain unknown. Therefore, the present study evaluates three physiological markers during 2018 (total lipid content, symbiont density, and chlorophyll a concentration) in the main reef-building coral genera (Pocillopora, Porites, and Pavona) from two coral communities: one coastal site next to a luxury touristic development with high sedimentation rates and elevated nutrient inputs from golf courses, and one at an insular MPA 6 km distant from the coast and where human activities are regulated. At each coral sampling site, nitrite, nitrate, and phosphate concentrations as well as sedimentation rates were measured. The analyses of the physiological markers showed significant differences in the lipid content and symbiont density between sites, with corals at Isla Larga presenting higher lipid content but lower symbiont density, while pigment concentration only differed across months. When assessing differences among coral genera, Pocillopora colonies presented the highest lipid content, while Pavona showed more symbionts and Porites colonies the uppermost pigment concentrations, with significant differences among genera and across the studied months. Environmental characterization showed significant differences between sites in the nitrate concentration and sedimentation rates. Generalized nonlinear models evidence that lipid concentration is related to sedimentation rates and temperatures, symbiont density to nitrite and phosphate concentrations, and pigment concentrations to nitrate and phosphate concentrations as well as sedimentation rates.

Coral reefs are of global concern in the face of increasing anthropogenic disturbance. Much research has focused on the negative factors associated with coral reef decline, but few have documented the positive factors in relation to recovering coral reefs. Here, we report a positive quantitative association between sea urchins (diadematids), coral recruitment and coral recovery, recorded along Taiwanese coral reefs. We monitored coral cover change, juvenile coral density, herbivore density (fishes, sea urchins, gastropods) and macroalgal cover, along three reefs between 2012 and 2015. Multivariable regression analyses revealed that sea urchin (diadematids) density was the primary (positive) driver, explaining 74% of variation in coral cover change and 89% in coral juvenile density among sites and years. The relationship between sea urchin density and coral juvenile density was especially evident for four common coral genera: Acropora, Dipsastraea, Pocillopora and Porites. These results suggest that diadematid urchins enhance coral recovery on these reefs by promoting the recruitment of corals. The density of juvenile corals was also found to explain 67% of variation in coral cover change, highlighting the potential use of coral juvenile density as a proxy for coral recovery potential in coral resilience studies.

The Hawaiian Islands are at the northern edge of coral reef distributions, and corals found there are exposed to large seasonal temperature changes. Historically, coral bleaching in the Hawaiian Islands was extremely rare and had only occurred in 1996. However, in the summers of both 2014 and 2015, successive bleaching events occurred in Kāne‘ohe Bay, O‘ahu. Seawater temperatures were above 28 °C for approximately 1 month in 2014 and 3 months in 2015 and peaked above 30 °C in both years. Patterns of bleaching did not vary among the three sites within Kāne‘ohe Bay. Severe bleaching and paling covered 77 and 55% of reefs in 2014 and 2015, respectively. Different species showed a range of susceptibility with 80–100% of Pocillopora spp. bleaching in both years, but less than 50% bleaching of Porites compressa and Montipora capitata in Kāne‘ohe Bay. Less than 1% of the encrusting coral Leptastrea purpurea colonies bleached in both years. Sixty individual colonies of P. compressa and M. capitata and 28 colonies of Pocillopora damicornis were tagged and monitored for rates of bleaching, recovery and mortality throughout the two-year period. Most of the colonies that bleached recovered their symbionts within 3–4 months, though P. compressa visually recovered more rapidly than M. capitata and P. damicornis. Cumulatively, 19% of P. damicornis, 10% of M. capitata and no P. compressa died by May 2016. Partial mortality within a colony did not occur in 2014, but impacted 13% of the colonies in 2015, with P. damicornis and M. capitata having higher rates of partial mortality than P. compressa. Relatively, low susceptibility in the dominant species and low rates of mortality combined with rapid rates of recovery show coral resilience to anomalously high temperatures in Kāne‘ohe Bay, O‘ahu.

Characterizations of colony-specific fate are necessary to predict trajectories of coral population change accurately, and a research challenge exists to collect more robust data describing coral demographic rates and the factors that influence them. Colonial, reef-building corals present challenges to the study of demography, given that the size of individual colonies can be decoupled from age, and rates of colony growth and shrinkage can be effectively indeterminate. In this study, we use a large-area imaging approach to quantify demographic rates of the coral genus Pocillopora and test for the influence of colony-specific predictors on net change in live tissue area (labeled growth and shrinkage) and whole-colony mortality. We found that a colony’s fate was linked to its initial size, with larger colonies experiencing far lower probability of mortality, but higher probability of shrinkage, than smaller colonies. Historical effects also significantly affected colony fate, as colonies with a recent history of tissue loss experienced a higher probability of subsequent shrinkage and mortality the following year. Finally, significant variability in growth and mortality rates was linked to intra-island site differences, which we hypothesize may be driven by differences in food availability and heterotrophic feeding rates. Our work highlights the importance of colony-specific characteristics, including size and historical effects, in influencing demographic fates of corals.

Widespread coral bleaching occurred in the central Red Sea in 2010 and 2015. During both events, a cross-shelf and depth gradient of bleaching severity was identified within the Thuwal reef system, central Red Sea, Saudi Arabia. While bleaching and survival of coral taxa were monitored, neither in situ reef temperatures nor coral-associated algal communities (family Symbiodiniaceae) were characterized. Here, we determined coral host-associated Symbiodiniaceae communities and monitored temperatures along the same cross-shelf and depth gradient on six reefs in 2017 to better understand the role of these factors in the observed bleaching patterns and to generate a baseline for further studies. We characterized > 600 coral–algal associations across winter and summer in six genera of scleractinian coral (Pocillopora, Stylophora, Seriatopora, Galaxea, Gardineroseris, and Porites) and one fire coral (Family Milleporidae) using ITS2 next-generation sequencing in conjunction with the SymPortal analytical framework. We show that previous bleaching patterns correlate poorly with the largely coral host-specific structure of the 2017 Symbiodiniaceae community and are in better agreement with absolute and intraday sea water temperature variations monitored on the reefs. We demonstrate a greater distinctiveness of Symbiodiniaceae communities at the more severely bleached inshore reefs compared to those reefs further offshore. However, the potential Symbiodiniaceae community changes at these reefs prior to our sampling prevent us from evaluating this distinctiveness as determinative of the differences in bleaching severities. Based on our analyses, we discuss how fine-scale delineation of algal genotypes, including host-specific putative genotypes of Durusdinium trenchii that represent alluring targets for further taxonomic identification, corroborate a niche-adapted rather than generalist character of many coral–Symbiodiniaceae associations. In conclusion, as studies such as this one continue to build the global catalogue of coral–Symbiodiniaceae associations, we may be afforded a better oversight of how specialized coral–algal associations really are and how restricted their modification may be, both of which are critical considerations in predicting the adaptive potential of corals and the reef ecosystems they build.

Reproduction and recruitment are essential processes for the continued success of coral communities. Islas Marias Archipelago is considered a connectivity node among coral communities distributed along the Northeastern Tropical Pacific (NTP); as such, sexual reproduction of scleractinian corals affects the maintenance of the local populations and the long-distance connectivity of reefs across the region. In this study, successful sexual reproduction in the species of the three most abundant scleractinian corals genera was demonstrated, in part by documenting gamete presence and maturation in tissues and spatio-temporal variability in juvenile coral settlement, which were quantified across substrate type, habitat quality, and environmental factors. Only 12 larvae recruited (ten Porites, two Pavona) to artificial substrates, and monthly recruitment density of 1.82 ± 0.23 recruits m−2 (n = 383) was recorded on natural substrates. There were significant differences between genera, with Porites producing the highest density of recruits (0.60 ± 0.45 recruits m−2, followed by Pavona (0.52 ± 0.24 recruits m−2) and Pocillopora (0.28 ± 0.06 recruits m−2). The highest coral recruitment was observed at Baby Reef (2.57 ± 0.46 recruits m−2), followed by Cleofas II (1.81 ± 0.21 recruits m−2) and Japanese Garden (1.24 ± 0.46 recruits m−2); the former site was characterized by the highest cover of crustose coralline algae. We found successful recruitment of the main reef-forming species in the Mexican Pacific and suggest that Islas Marias is a region of critical importance in terms of its function as a source of genetic variability, and, the generation of, new individuals that will be key to sustaining coral reef ecosystems in the NTP.

Repeated bouts of coral bleaching threaten the long-term persistence of coral reefs and associated communities. Here, we document the short- and long-term impacts of heatwave events on coral and fish assemblages, based on regular surveys of 18 reefs of the granitic islands of Seychelles over 23 yr. Extreme heat events in 1998 and 2016 led to bleaching-associated declines in coral cover, whilst between these years there was an interim period of coral recovery on some reefs. Coral decline and recovery were primarily due to changes in the cover of branching coral, particularly those from the families Acroporidae and Pocilloporidae. Surveys during the 2016 bleaching found that 95% of the 468 Acropora and Pocillopora colonies observed were either bleached or recently dead. The extent of bleaching and subsequent mortality were best explained by a priori assessments of community susceptibility to heat stress. One year later (2017), coral cover had fallen by 70% and average coverage across the 18 reefs was at 6%, similar to levels recorded in 2005, 7 yr after the 1998 bleaching. Decline in coral following the 2016 bleaching coincided with reduced abundance of fish < 11 cm TL, particularly corallivores, invertivores and mixed diet feeders. These changes are likely to foreshadow more widespread loss once the habitat structure erodes. Accordingly, 7 yr after the 1998 bleaching, when coral skeletons and reef structure had collapsed on some reefs, abundance of both large- and small-bodied fish had declined. We show that fluctuation in the cover of branching coral is positively associated with changes in the abundance of small-bodied fish which contribute to ecological processes and high diversity, suggesting branching corals are a keystone structure. Increased frequency of bleaching threatens the capacity of branching corals to fully recover after disturbances, reducing the amplitude of boom bust cycles of these corals and the keystone habitat structure they provide reef fish.

Extensive phenotypic plasticity generally confounds identification of the common reef-building coral Pocillopora damicornis. With the recognition of P. damicornis genetic lineages as taxonomic species, this study surveyed genetic lineages within P. damicornis sensu lato (Veron and Pichon in Scleractinia of Eastern Australia, Australian Institute of Marine Science, Australia, 1976) in the Philippines. Employing a PCR–RFLP assay of the mitochondrial control region and sequencing of the mitochondrial open reading frame for lineage identification, we examined 694 P. damicornis s.l. colonies from 16 locations across the Philippine archipelago to characterize Pocillopora species distribution in the region. Genetic identification reveals the occurrence of P. acuta and the absence of P. damicornis in the Philippines. This study highlights the need to revisit the distributional limits of this extensively studied species complex and the necessity of using genetic information for taxonomic identification where morphological identification is unreliable.

High densities of two corallivorous gastropods, Drupella cornus and D. rugosa, may delay the recovery of coral reefs impacted by mass bleaching events by aggregating on the remaining corals. Following severe bleaching in April/May 2016 that resulted in the loss of up to 80% of the living coral cover from reefs in South Male, Maldives, aggregations of up to 250 Drupella per coral were recorded on surviving colonies. The distribution of snails was not random; larger aggregations were seen on reefs with fewer remaining live corals and also on the largest corals. Branching, digitate and tabular corals, especially species of Acropora and Pocillopora, sustained the highest mortality from the bleaching. Remaining colonies of these taxa exhibited the highest occurrence of snails and the most extensive snail predation, although less-preferred taxa such as Montipora, Porites, Astreopora, Cyphastrea and Pachyseris were also targeted. Drupella also concentrated on broken Acropora branches and overturned colonies; on some reefs, these were the only surviving acroporids, and many of them did not bleach. Continued predation pressure from Drupella may eliminate formerly dominant corals, including genets that are resistant to higher sea water temperatures.

Numerous seaweeds produce secondary metabolites that are allelopathic to corals. To date, most of the compounds identified in this interaction are lipid-soluble instead of water-soluble. Thus, understanding whether these compounds are stored internally where they would not contact corals, or occur on external surfaces where they could be transferred to corals, is critical to understanding seaweed–coral interactions and to informing realistic experiments on chemically mediated interactions. We conducted field experiments assessing the effects of lipid-soluble extracts from macroalgal surfaces alone versus total lipid-soluble extracts from both internal and external tissues on the coral Pocillopora verrucosa. Extracts of the red algae Amansia rhodantha and Asparagopsis taxiformis, the green alga Chlorodesmis fastigiata, and the brown alga Dictyota bartayresiana suppressed coral photochemical efficiency; in these bioactive species, the total lipid-soluble extracts were not more potent than surface-only extracts despite the concentration of total extracts being many times greater than surface-only extracts. This suggests that previous assays with total extracts may be ecologically meaningful, but also that future assays should be conducted with the simpler, less concentrated, and more ecologically relevant surface extracts. Allelopathic effects of As. taxiformis and C. fastigiata were significantly greater than the effect of D. bartayresiana, with effects of Am. rhodantha intermediate between these groups. Neither surface-only nor total lipid-soluble extracts of the seaweed Turbinaria ornata were allelopathic, and its lack of potency differed significantly from all other species. Our results suggest that lipid-soluble, allelopathic compounds are usually deployed on seaweed surfaces where they can be effective in surface-mediated interactions against other species.

Coral recruitment and juvenile growth are essential processes for coral population maintenance and recovery. A growing body of research has evaluated the influence of reef microstructure on coral settlement and post-settlement survival, showing that physical refugia enhance recruitment. These studies have evaluated coral recruit morality from competition with macroalgae and indirect predation by grazing organisms, but the impact of direct predation by corallivorous piscine species on juvenile corals and how this interacts with reef microstructure is relatively unknown. This study examined whether refugia provided by micro-crevices enhance juvenile coral survival from corallivory. Juvenile corals from two different functional groups, the slow-growing massive Porites lobata and fast-growing branching Pocillopora damicornis, with average nubbin sizes of 1.4 cm × 0.3 cm and 0.5 cm × 1.0 cm (diameter × height), respectively, were attached to experimental tiles using small (1.44 cm3) and large (8.0 cm3) crevice sizes and were monitored for 29 d on a forereef in Palau. Full crevices (four sided) enhanced coral survival compared to exposed microhabitats in both coral taxa, but crevice size did not alter survival rates. Corallivores targeted recruits within crevices regardless of crevice size; dominant predators included small triggerfish (Balistidae), butterflyfish (Chaetodon), and wrasse (Cheilinus). Overall, Pocillopora suffered much higher rates of mortality than Porites. All Pocillopora were consumed by day 8 of the experiment, but mortality was significantly delayed in full crevices compared to exposed and partial crevice (three sided) microhabitats. In contrast, Por. lobata located in all microhabitats survived the entire experiment up to 29 d, with high survival in full (>90%) and partial crevices (70%), but only 28% survival in exposed microhabitats. These findings show the importance of crevices as spatial refugia from predators for juvenile corals and highlight the importance of structural complexity for juvenile coral growth and survival that enhances reef recovery.

Studies on the population and community dynamics of scleractinian corals typically focus on catastrophic mortality associated with acute disturbances (e.g., coral bleaching and outbreaks of crown-of-thorns starfish), though corals are subject to high levels of background mortality and injuries caused by routine and chronic processes. This study quantified prevalence (proportion of colonies with injuries) and severity (areal extent of injuries on individual colonies) of background mortality and injuries for four common coral taxa (massive Porites, encrusting Montipora, Acropora hyacinthus and branching Pocillopora) on the Great Barrier Reef, Australia. Sampling was conducted over three consecutive years during which there were no major acute disturbances. A total of 2276 adult colonies were surveyed across 27 sites, within nine reefs and three distinct latitudinal sectors. The prevalence of injuries was very high (>83%) across all four taxa, but highest for Porites (91%) and Montipora (85%). For these taxa (Montipora and Pocillopora), there was also significant temporal and spatial variation in prevalence of partial mortality. The severity of injuries ranged from 3% to more than 80% and varied among coral taxa, but was fairly constant spatially and temporally. This shows that some injuries have considerable longevity and that corals may invest relatively little in regenerating tissue over sites of previous injuries. Inter-colony variation in the severity of injury also had no apparent effect on the realized growth of individual colonies, suggesting that energy diverted to regeneration has a limited bearing on overall energetic allocation, or impacts on other life-history processes (e.g., reproduction) rather than growth. Establishing background levels of injury and regeneration is important for understanding energy investment and life-history consequences for reef-building corals as well as for predicting susceptibility to, and capacity to recover from, acute disturbances.

Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

Phylogenetic evidence indicates that Siderastrea glynni, a species of coral thought to be endemic to the Eastern Pacific, is actually more likely to be Si. siderea introduced from the Atlantic. Our analyses of the endosymbionts of Si. glynni (Symbiodinium) substantiate this as an introduced species; attempts to conserve and list Si. glynni as an endangered species are probably unwarranted. The specimens we examined harbored Symbiodinium trenchii and some also contained Sy. goreaui, symbionts that occur with Si. siderea in the Atlantic. Moreover, the genotype of Sy. trenchii (a single strain defined by ten diallelic microsatellite loci) was genetically distinct from genotypes of Sy. ‘glynni,’ also in Clade D, found abundantly in colonies of Pocillopora throughout the region. Furthermore, the strain of Sy. trenchii grouped with genotypes from the Greater Caribbean, an inbred population that was recently introduced from the Indo-West Pacific. This secondary introduction suggests that strains of Caribbean Sy. trenchii are capable of dispersal into new reef coral communities where this symbiont does not presently exist.

Dendropoma maximum is a vermetid gastropod (a sessile tube-forming snail) commonly associated with living corals throughout shallow-water reefs of the Indo- Pacific. Recent work suggests that, once established, this species can adversely affect growth and survival of corals. Here, we test the hypotheses that disturbances to live coral substrates (e.g., creation of bare patches) facilitate suc- cessful larval settlement and subsequent population growth of D. maximum, and conversely, that live coral inhibits D. maximum settlement. In the shallow lagoon of Moorea, French Polynesia, we selected patch reefs where D. maxi- mum was either present or absent (to evaluate potential effects of resident adult conspecifics on recruitment) and established focal quadrats on each reef. In each quadrat, we either experimentally removed 50 % of live coral cover or left the quadrat with 100 % live coral cover. In addition, we deployed units of bare substrate (coral rubble) to each reef. We conducted a census of deployed substrates and quadrats after 6 months and found that D. maximum settled irrespective of resident vermetid populations, and only onto nonliving surfaces (i.e., cleared patches in quadrats, coral rubble, and marine epoxy). In laboratory experiments, we exposed larvae of D. maximum to live coral and found species-specific effects on survival of D. maximum larvae. Porites lobata and Pocillopora sp. killed larvae of D. maximum, Porites rus caused weaker mortality, and Millepora sp. had no effect on larval survival. Collectively, these results suggest that D. maximum requires distur- bances that create bare patches to successfully settle onto reefs, and that a high cover of living corals contributes resilience to reefs by limiting settlement opportunities of a species known to reduce coral growth and survival.

This study examined the effects of the Guineafowl pufferfish (Arothron meleagris), a major corallivore in the Eastern Pacific, on pocilloporid corals on a reef at Gorgona Island, Colombia. Pufferfish occurred at a density of 171.2 individuals ha−1 and fed at a rate of 1.8 bites min−1, which produced a standing bite density of 366.2 bites m−2. We estimate that approximately 15.6 % of the annual pocilloporid carbonate production is removed by the pufferfish population. Examination of the predation effect on individual pocilloporid colonies revealed that although nubbins exposed to corallivory had lower linear growth, they gained similar weight and became thicker than those protected from it. Additionally, colonies with simulated predation injuries (on up to 75 % of branch tips) healed successfully and maintained growth rates similar to those of uninjured colonies. Despite the high corallivore pressure exerted by pufferfish on this reef, we conclude that they have a low destructive impact on Pocillopora colonies as corals can maintain their carbonate production rate while effectively recovering from partial predation. Due to its influence on colony morphology, pufferfish predation may increase environmentally induced morphological variability in Pocillopora.

Corals in the genus Pocillopora are the primary framework builders of eastern tropical Pacific (ETP) reefs. These corals typically associate with algal symbionts (genus Symbiodinium) in clade C and/or D, with clade D associations having greater thermal tolerance and resistance to bleaching. Recently, cryptic "species" delineations within both Pocillopora and Symbiodinium have been suggested, with host–symbiont specificity used as a supporting taxonomic character in both genera. In particular, it has been suggested that three lineages of Pocillopora (types 1–3) exist in the ETP, of which type 1 is the exclusive host of heat-tolerant Symbiodinium D1. This host specificity has been used to support the species name "Symbiodinium glynni" for this symbiont. To validate these host–symbiont relationships and their taxonomic utility, we identified Pocillopora types and their associated Symbiodinium at three sites in the ETP. We found greater flexibility in host–symbiont combinations than previously reported, with both Pocillopora types 1 and 3 able to host and be dominated by Symbiodinium in clade C or D. The prevalence of certain combinations did vary among sites, showing that a gradient of specificity exists which may be mediated by evolutionary relationships and environmental disturbance history. However, these results limit the utility of apparent host–symbiont specificity (which may have been a result of undersampling) in defining species boundaries in either corals or Symbiodinium. They also suggest that a greater diversity of corals may benefit from the thermal tolerance of clade D symbionts, affirming the need to conserve Pocillopora across its entire geographic and environmental range.

The contributions of sexual versus asexual reproduction are thought to play an important role in the abundance and ecological success of corals, especially in marginal habitats. Pocillopora corals are distributed throughout the Indo-Pacific and dominate shallow hard-bottom communities in the eastern Pacific where broad seasonal fluctuations in temperature and water turbidity create suboptimal conditions for reef community development. Previous work had revealed three genetic clades in the eastern Pacific that show little correspondence with colony morphology; the broad distribution of type 1 extends into the subtropical southern Gulf of California. Here we examine genetic and clonal structure of two type 1 communities separated by 10 km with microsatellite data. Samples were collected randomly in six 10 m radius circular plots (20 colonies per plot, 3 plots per site). Sites differed in their relative clonality because clonemates (ramets) from a single clone (genet) dominated a large portion (90.9 m long) of the protected leeward side of Gaviota Island (Number of genets/Number of samples = 0.35; observed Genotypic diversity/expected Genotypic diversity = 0.087), while an exposed community at the entrance to La Paz Bay, Punta Galeras, exhibited high genotypic diversity (Ng/N = 0.85; Go/Ge = 0.714). Gene flow was unrestricted between sites indicating these communities comprised a single population. The relative proportion of asexual colonies found between community aggregations of Pocillopora in the Gulf of California differed significantly and suggests factors at local, not regional, scales affect these patterns. The possibility that heterogeneity in clonal structure is common throughout the eastern Pacific and across the west Indo-Pacific requires further study. Finally, since morphological variation in Pocillopora has been underappreciated and is in need of taxonomic revision, the use of a consistent field-sampling protocol and high-resolution makers will advance ecological research and aid in the conservation of these corals.

Ecological patterns are created by processes acting over multiple spatial and temporal scales. By com- bining spatially explicit sampling with variance compo- nents models, the relative importance of spatial scale to overall variability can be determined. We used a spatially structured experimental design in the Mombasa Marine National Park in Kenya to quantify variation in coral recruitment across four spatial scales (*1-1,000 m) and to generate hypotheses about processes affecting recruitment and potential sources of post-settlement mortality during early life history. For the dominant recruiting corals (Pocillopora spp.), variation in recruitment on surfaces protected from fish grazing was greatest at the largest spatial scale examined (1,000 m). We hypothesize that recruitment on protected surfaces varies mainly with larval delivery due to different lagoonal circulation and water flow between sites. Conversely, variation on surfaces exposed to fishes was greatest at the smallest spatial scale (1 m). We hypothesize that recruitment on exposed sur- faces mainly reflects local differences in the scale and intensity of fish grazing, which may obscure larval delivery patterns. Spatial variation in recruitment can affect many ecological processes and factors, including growth, sur- vival to maturity, the distribution of habitat, and variation in species interaction strengths. This study demonstrates how spatially explicit sampling, followed by variance components modeling to partition variance across scales, can help to identify potential drivers of patterns at each relevant scale.

Physiologically distinct lines of dinoflagellate symbionts, Symbiodinium spp., may confer distinct thermal tolerance thresholds on their host corals. Therefore, if a coral can alternately host distinct symbionts, changes in their Symbiodinium communities might allow corals to better tolerate increasing environmental temperatures. However, researchers are currently debating how commonly coral species can host different symbiont types. We sequenced chloroplast 23 s rDNA from the Symbiodinium communities of nine reef-building coral species across two thermally distinct lagoon pools separated by ~500 m. The hotter of these pools reaches 35°C in the summer months, while the other pool’s maximum temperature is 1.5°C cooler. Across 217 samples from nine species, we found a single haplotype in both Symbiodinium clades A and D, but four haplotypes in Symbiodinium clade C. Eight of nine species hosted a putatively thermally resistant member of clade D Symbiodinium at least once, one of which hosted this clade D symbiont exclusively. Of the remaining seven that hosted multiple Symbiodinium types, six species showed higher proportions of the clade D symbiont in the hotter pool. Average percentage rise in the frequency of the clade D symbiont from the hotter to cooler pool was 52% across these six species. Even though corals hosted members of both the genetically divergent clades D and C Symbiodinium, some showed patterns of host–symbiont specificity within clade C. Both Acropora species that hosted clade C exclusively hosted a member of sub-clade C2, while all three Pocillopora species hosted a member of sub-clade C1 (sensu van Oppen et al. 2001). Our results suggest that coral–algal symbioses often conform to particular temperature environments through changes in the identity of the algal symbiont.

Stony corals provide important structural habitat for microbes, invertebrates, and fishes, which in some cases has led to the evolution of beneficial interactions that may protect corals from environmental factors such as thermal stress, nutrient limitation, competitors, or predators. For example, guard crabs (Trapezia spp.) protect corals (Pocillopora sp.) from attacks by crown-of-thorn seastar and sedimentation. Here, a field experiment demonstrates that guard crabs (Trapezia serenei) also ameliorate the strong negative effects of the giant vermetid (Dendropoma maximum) on growth of Pocillopora. This experiment highlights the importance of this crab-coral mutualism: guard crabs facilitate the growth of corals in stressful environments (e.g., where vermetids are abundant), thereby preserving the ecological goods and services (e.g., food and shelter) that these corals may provide to other reef-associated species.

Particulate organic matter (POM) and dissolved organic carbon (DOC) release by six dominant hermatypic coral genera (Acropora, Fungia, Goniastrea, Millepora, Pocillopora and Stylophora) were measured under undisturbed conditions by laboratory incubations during four seasonal expeditions to the Northern Red Sea. In addition, the influence of environmental factors (water temperature, light availability and ambient inorganic nutrient concentrations) was evaluated. Particulate organic carbon (POC) and particulate nitrogen (PN) release were always detectable and genus-specific, with Stylophora releasing most POM (6.5 mg POC and 0.5 mg PN m−2 coral surface area h−1) during all seasons. The fire coral Millepora released significantly less POM (0.3 mg POC and 0.04 mg PN m−2 coral surface area h−1) than all investigated anthozoan genera. The average POC:PN ratio of POM released by all coral genera was 12 ± 1, indicating high carbon/low nitrogen content of coral-derived organic matter. POM release showed little seasonal variation, but average values of POC and PN release rates correlated with water temperature, light availability and ambient nitrate concentrations. DOC net release and elevated DOC:POC ratios were detectable for Acropora, Goniastrea and Millepora, revealing maximum values for Acropora (30.7 mg DOC m−2 coral surface area h−1), whilst predominant DOC uptake was observed for Pocillopora, Fungia and Stylophora. Depth-mediated light availability influenced DOC fluxes of Acropora and Fungia, while fluctuations in water temperature and ambient inorganic nutrient concentrations showed no correlation. These comprehensive data provide an important basis for the understanding of coral reef organic matter dynamics and relevant environmental factors.

Surveys of microsatellite variation show that genetic diversity has largely recovered in two reef-building corals, Pocillopora damicornis and Seriatopora hystrix (Scleractinia: Pocilloporidae), on reefs which were decimated by the eruption of the volcano Krakatau in 1883. Assignment methods and gene flow estimates indicate that the recolonization of Krakatau occurred mainly from the closest upstream reef system, Pulau Seribu, but that larval input from other regions has also occurred. This pattern is clearer in S. hystrix, which is traditionally the more dispersal-limited species. Despite these observed patterns of larval dispersal, self-recruitment appears to now be the most important factor in supplying larvae to coral populations in Krakatau. This suggests that the colonization of devastated reefs can occur quickly through larval dispersal; however, their survival requires local sources of larvae for self-recruitment. This research supports the observation that the recovery of genetic diversity in coral reef animals can occur on the order of decades and centuries rather than millennia. Conservation measures aimed at sustaining coral reef populations in Krakatau and elsewhere should include both the protection of upstream source populations for larval replenishment should disaster occur as well as the protection of large adult colonies to serve as local larval sources.

Here we report a highly variable nuclear marker that can be used for both soft and stony corals. Primers that amplify a ∼177 bp fragment from the nuclear gene encoding the 54 kDa subunit of the signal recognition particle (SRP54) were developed for the octocoral genus Carijoa. Cloning results from 141 individuals suggest that this hypervariable nuclear locus is a single-copy gene. Sequencing revealed a potential cryptic species previously thought to be Carijoa riisei. Results from an Analysis of Molecular Variance (AMOVA) based on mitochondrial DNA (mtDNA) explained 33% of the variation (Fst = 0.54). Using previously reported degenerate primers for SRP54, high levels of sequence variation were found at this locus across both scleractinian and octocorals. For example, pairwise sequence divergence within octocorals was ∼8–13 times greater with SRP54 than with mtDNA, and, up to 2.8% pairwise sequence divergence was found in SRP54 among individuals of Pocillopora whereas no variation at all was found in mtDNA markers. This case study with the octocoral C. riisei shows that variation in SRP54 appears sufficient to address questions of phylogeography as well as systematics of closely related species.

A mild bleaching event was observed among Pocillopora spp. in the southern Gulf of California in the spring of 2006. Uniform bleaching occurred in numerous colonies on the upper portions of their branches. Most (∼90%) colonies that exhibited bleaching contained a species of endosymbiotic dinoflagellate, Symbiodinium C1b-c, which differed from the Symbiodinium D1 found inhabiting most unbleached colonies. Analysis of chlorophyll fluorescence, indicated a decline in photosystem II photochemical activity, especially among colonies populated with C1b-c. By early August, most affected colonies had recovered their normal pigmentation and fluorescence values were once again high for all colonies. No mortality was observed among tagged bleached colonies nor did symbiont species composition change during recovery. This unusual episode of bleaching did not appear to be a response to thermal stress, but may have been triggered by high levels of solar radiation during a period of unseasonally high water clarity in the early spring.

We have investigated the relationship between genotypic diversity, the mode of production of brooded larvae and disturbance in a range of reef habitats, in order to resolve the disparity between the reproductive mode and population structure reported for the brooding coral Pocillopora damicornis. Within 14 sites across six habitats, the ratio of the observed (G o) to the expected (G e) genotypic diversity ranged from 69 to 100% of that expected for random mating. At three other sites in two habitats the G o /G e ranged from 35 to 53%. Two of these sites were recently bleached, suggesting that asexual recruitment may be favoured after disturbance. Nevertheless, our data suggest that brooded larvae, from each of five habitats surveyed, were asexually produced. While clonal recruitment may be important in disturbed habitats, the lack of clonality detected, both in this and earlier surveys of 40 other sites, implies that a disturbance is normally insufficient to explain this species’ continued investment in clonal reproduction.

The fringing reef off southern Molokai, Hawaii, is currently being studied as part of a multi-disciplinary project led by the US Geological Survey. As part of this study, modeling and field observations were utilized to help understand the physical controls on reef morphol- ogy and the distribution of different coral species. A model was developed that calculates wave-induced hydrodynamic forces on corals of a specific form and mechanical strength. From these calculations, the wave conditions under which specific species of corals would either be stable or would break due to the imposed wave- induced forces were determined. By combining this hydrodynamic force-balance model with various wave model output for different oceanographic conditions experienced in the study area, we were able to map the locations where specific coral species should be stable (not subject to frequent breakage) in the study area. The combined model output was then compared with data on coral species distribution and coral cover at 12 sites along Molokai's south shore. Observations and model- ing suggest that the transition from one coral species to another may occur when the ratio of the coral colony's mechanical strengths to the applied (wave-induced) forces may be as great as 5:1, and not less than 1:1 when corals would break. This implies that coral colony's mechanical strength and wave-induced forces may be important in defining gross coral community structure over large (orders of 10's of meters) spatial scales.