Mass brooding of the blue octocoral,Heliopora coerulea on a sedimented equatorial reef

The octocoral Heliopora coerulea is a gonochoric surface brooder. Although the species is common on shallow Indo-Pacific coral reefs, information on its reproductive biology is limited and spawning timings have only been reported from four locations. We report the first observations of surface brooding in H. coerulea on a sedimented equatorial reef. In April 2014, 46 and 26 brooding colonies were recorded, respectively, from reefs fringing the islands of Kusu and Lazarus in Singapore. The brooded coral larvae were tightly bound to inflated coral polyps, forming a dense white mat which blanketed the brown coral tissue. The inflated polyps also protruded from layers of sediment, which accumulated in colony crevices, such that the brooded larvae were elevated above the settled sediment. Our observations supplement existing knowledge on the reproductive timing of H. coerulea and highlight the adaptations that improve survival of this species on sediment-impacted reefs.     

The non-linear relationship between body size and function in parrotfishes

Parrotfishes are a group of herbivores that play an important functional role in structuring benthic communities on coral reefs. Increasingly, these fish are being targeted by fishermen, and resultant declines in biomass and abundance may have severe consequences for the dynamics and regeneration of coral reefs. However, the impact of overfishing extends beyond declining fish stocks. It can also lead to demographic changes within species populations where mean body size is reduced. The effect of reduced mean body size on population dynamics is well described in literature but virtually no information exists on how this may influence important ecological functions. The study investigated how one important function, scraping (i.e., the capacity to remove algae and open up bare substratum for coral larval settlement), by three common species of parrotfishes (Scarus niger, Chlorurus sordidus, and Chlorurus strongylocephalus) on coral reefs at Zanzibar (Tanzania) was influenced by the size of individual fishes. There was a non-linear relationship between body size and scraping function for all species examined, and impact through scraping was also found to increase markedly when fish reached a size of 15–20 cm. Thus, coral reefs which have a high abundance and biomass of parrotfish may nonetheless be functionally impaired if dominated by small-sized individuals. Reductions in mean body size within parrotfish populations could, therefore, have functional impacts on coral reefs that previously have been overlooked.     

Maintenance of fish diversity on disturbed coral reefs

Habitat perturbations play a major role in shaping community structure; however, the elements of disturbance-related habitat change that affect diversity are not always apparent. This study examined the effects of habitat disturbances on species richness of coral reef fish assemblages using annual surveys of habitat and 210 fish species from 10 reefs on the Great Barrier Reef (GBR). Over a period of 11 years, major disturbances, including localised outbreaks of crown-of-thorns sea star (Acanthaster planci), severe storms or coral bleaching, resulted in coral decline of 46–96% in all the 10 reefs. Despite declines in coral cover, structural complexity of the reef framework was retained on five and species richness of coral reef fishes maintained on nine of the disturbed reefs. Extensive loss of coral resulted in localised declines of highly specialised coral-dependent species, but this loss of diversity was more than compensated for by increases in the number of species that feed on the epilithic algal matrix (EAM). A unimodal relationship between areal coral cover and species richness indicated species richness was greatest at approximately 20% coral cover declining by 3–4 species (6–8% of average richness) at higher and lower coral cover. Results revealed that declines in coral cover on reefs may have limited short-term impact on the diversity of coral reef fishes, though there may be fundamental changes in the community structure of fishes.     

Recruitment and larval connectivity of a remnant Acropora community in the Arabian Gulf,United Arab Emirates

Coral cover and community structure in the Arabian Gulf have changed considerably in recent decades. Recurrent bleaching events have dramatically reduced the abundance of previously dominant Acropora corals and have given space to other more thermally resistant coral taxa. The loss of Acropora spp. has reduced reef structural complexity and associated biodiversity. Sir Bu Nair Island (SBN) is a nature reserve in the United Arab Emirates that sustains some of the last dense and extensive Acropora stands in the southern Gulf. This study investigated coral recruitment at a southern coral reef on SBN and examined larval dispersal and reef connectivity between SBN and other local and regional reefs through an agent-based model coupled with a 3D hydrodynamic model. Recruitment was surveyed with settlement tiles deployed from April to September 2019. Contrary to other reefs in the Gulf, we found that Acropora is indeed the major coral recruiter settling at SBN reefs, followed by Porites. The models indicate that SBN reefs are mostly self-seeding but also connected to other reefs in the Gulf. SBN can supply coral larvae to the neighbouring islands Siri and Abu Musa, and nearby reefs along with the north-eastern Emirates, Iranian coast and Strait of Hormuz. Findings highlight the importance of SBN to protect remnant populations of the locally almost extinct Acropora in a region where natural coral recovery is increasingly sparse.

     

Coral reef crisis in deep and shallow reefs: 30 years of constancy and change in reefs of Curacao and Bonaire

Coral reefs are thought to be in worldwide decline but available data are practically limited to reefs shallower than 25 m. Zooxanthellate coral communities in deep reefs (30–40 m) are relatively unstudied. Our question is: what is happening in deep reefs in terms of coral cover and coral mortality? We compare changes in species composition, coral mortality, and coral cover at Caribbean (Curacao and Bonaire) deep (30–40 m) and shallow reefs (10–20 m) using long-term (1973–2002) data from permanent photo quadrats. About 20 zooxanthellate coral species are common in the deep-reef communities, dominated by Agaricia sp., with coral cover up to 60%. In contrast with shallow reefs, there is no decrease in coral cover or number of coral colonies in deep reefs over the last 30 years. In deep reefs, non-agaricid species are decreasing but agaricid domination will be interrupted by natural catastrophic mortality such as deep coral bleaching and storms. Temperature is a vastly fluctuating variable in the deep-reef environment with extremely low temperatures possibly related to deep-reef bleaching. An erratum to this article can be found at     

The influence of coral reef benthic condition on associated fish assemblages

Accumulative disturbances can erode a coral reef's resilience, often leading to replacement of scleractinian corals by macroalgae or other non-coral organisms. These degraded reef systems have been mostly described based on changes in the composition of the reef benthos, and there is little understanding of how such changes are influenced by, and in turn influence, other components of the reef ecosystem. This study investigated the spatial variation in benthic communities on fringing reefs around the inner Seychelles islands. Specifically, relationships between benthic composition and the underlying substrata, as well as the associated fish assemblages were assessed. High variability in benthic composition was found among reefs, with a gradient from high coral cover (up to 58%) and high structural complexity to high macroalgae cover (up to 95%) and low structural complexity at the extremes. This gradient was associated with declining species richness of fishes, reduced diversity of fish functional groups, and lower abundance of corallivorous fishes. There were no reciprocal increases in herbivorous fish abundances, and relationships with other fish functional groups and total fish abundance were weak. Reefs grouping at the extremes of complex coral habitats or low-complexity macroalgal habitats displayed markedly different fish communities, with only two species of benthic invertebrate feeding fishes in greater abundance in the macroalgal habitat. These results have negative implications for the continuation of many coral reef ecosystem processes and services if more reefs shift to extreme degraded conditions dominated by macroalgae.     

Analysis on variation trend of coral reef in Xisha

Xisha Islands, located in the northern part of South China Sea, consist of more than 20 islands and atolls. The coral reef of Xisha Islands belongs to the typical ocean distribution of world’s coral reefs, its ecosystem is the most typical in our country and hermatypic coral species are about three-quarters of the total coral species in China. It is addressed with the oldest coral reef community which of the most original and valuable in China. The previous research shows that the islands studded in South China Sea such as Xisha Islands have important influence on the formation of coral reefs along the mainland coast by multiplying and migrating from south to the north. It is supplementary sources of coastal coral larvae in Hainan and Guangdong. Therefore, carrying out the monitoring of coral reef community ecosystem is of great significance to the ecological protection. By the Manta tow and the Line Intercept Transect method, five stations (Xisha Yong xing dao, Shi dao, Xisha zhou, Zhao Shu dao and Bei dao) on Xisha ecological monitoring area were monitored continually from 2005 to 2009. We compared the index changes of Hermatypic coral’s species, coverage and recruitment, and combining with Condition Index, Succession Index, and the variation trend of hard coral in Xisha were analyzed.
The results show that, from 2005 to 2009, the coverage of living hermatypic corals in ecological monitoring area is sharply reduced from 68.19% to 7.93%, while the dead coral coverage is sharply increased from 4.70% to 72.90%. Coral recruitment is reduced from 1.18 ind/100 m² to 0.07 ind/100 m², hermatypic coral species decreased from 87 to 35. In 2005, the health of coral reefs was very good, and the Condition Index was 1.097. However, the Condition Index cut down to a very low degree in 2009. It was only ?0.880. The Succession Index belonged to “very low degree” from 2005 to 2009, and the numerical value was gradually reduce from ?0.984 to ?1.876.
As a whole, hermatypic corals are serious degrade regionally and caused great change to the coral structure and biodiversity, this will lead to a continuous degradation of coral reefs.     

Coral associations of the Pleistocene Ironshore Formation,Grand Cayman

The 125-ka sea level, which was approximately 6 m above present-day sea level, led to the partial flooding of many Caribbean islands. On Grand. Cayman, this event led to the formation of the large Ironshore Lagoon that covered most of the western half of the island and numerous, small embayments along the south, east, and north coasts. At that time, at least 33 coral species grew in waters around Grand Cayman. This fauna, like the modern coral fauna of Grand Cayman, was dominated byMontastrea annularis, Porites porites, Acropora polmata, andA. cervicornis. Scolymia cubensis andMycetophyllia ferox, not previously identified from the Late Pleistocene, are found in the Pleistocene patch reefs.Madracis mirabilis, Colpophyllia breviserialis, Agaricia tenuifolia, A. lamarcki, A. undata, Millepora spp., Mycetophyllia reesi, M. aliciae, andM. danaana, found on modern reefs, have not been identified from the Late Pleistocene reefs. Conversely,Pocillopora sp. cf.P. palmata, which is found in Late Pleistocene reefs, is absent on the modern reefs around Grand Cayman. The corals in the Ironshore Formation of Grand Cayman have been divided into 10 associations according to their dominant species, overall composition, and faunal diversity. Many of these associations are similar to the modern associations around Grand Cayman. Each of the Pleistocene coral associations, which can be accurately located on the known Late Pleistocene paleogeography of Grand Cayman, developed in distinct environmental settings. Overall trends identified in the modern settings are also apparent in the Late Pleistocene faunas. Thus, the diversity of the coral faunas increased from the interior of the Ironshore Lagoon to the reef crest. Similarly, the coral diversity in the Pleistocene patch reefs was related to the size of the reefs and their position relative to breaks in the barrier reef. The barrier reef included corals that are incapable of sediment rejection; whereas the patch reefs lacked such corals.     

Indirect consequences of fishing: reduction of coralline algae suppresses juvenile coral abundance

Removing predatory fishes has effects that cascade through ecosystems via interactions between species and functional groups. In Kenyan reef lagoons, fishing-induced trophic cascades produce sea urchin-dominated grazing communities that greatly reduce the overall cover of crustose coralline algae (CCA). Certain species of CCA enhance coral recruitment by chemically inducing coral settlement. If sea urchin grazing reduces cover of settlement-inducing CCA, coral recruitment and hence juvenile coral abundance may also decline on fished reefs. To determine whether fishing-induced changes in CCA influence coral recruitment and abundance, we compared (1) CCA taxonomic compositions and (2) taxon-specific associations between CCA and juvenile corals under three fisheries management systems: closed, gear-restricted, and open-access. On fished reefs (gear-restricted and open-access), abundances of two species of settlement-inducing CCA, Hydrolithon reinboldii and H. onkodes, were half those on closed reefs. On both closed and fished reefs, juveniles of four common coral families (Poritidae, Pocilloporidae, Agariciidae, and Faviidae) were more abundant on Hydrolithon than on any other settlement substrate. Coral densities were positively correlated with Hydrolithon spp. cover and were significantly lower on fished than on closed reefs, suggesting that fishing indirectly reduces coral recruitment or juvenile success over large spatial scales via reduction in settlement-inducing CCA. Therefore, managing reefs for higher cover of settlement-inducing CCA may enhance coral recruitment or juvenile survival and help to maintain the ecological and structural stability of reefs.     

Expansion of corals on temperate reefs: direct and indirect effects of marine heatwaves

Globally, many temperate marine communities have experienced significant temperature increases over recent decades in the form of gradual warming and heatwaves. As a result, these communities are shifting towards increasingly subtropical and tropical species compositions. Expanding coral populations have been reported from several temperate reef ecosystems along warming coastlines; these changes have been attributed to direct effects of gradual warming over decades. In contrast, increases in coral populations following shorter-term extreme warming events have rarely been documented. In this study, we compared coral populations on 17 temperate reefs in Western Australia before (2005/06) and after (2013) multiple marine heatwaves (2010–2012) affected the entire coastline. We hypothesised that coral communities would expand and change as a consequence of increasing local populations and recruitment of warm-affinity species. We found differences in coral community structure over time, driven primarily by a fourfold increase of one local species, Plesiastrea versipora, rather than recruitment of warm-affinity species. Coral populations became strongly dominated by small size classes, indicative of recent increased recruitment or recruit survival. These changes were likely facilitated by competitive release of corals from dominant temperate seaweeds, which perished during the heatwaves, rather than driven by direct temperature effects. Overall, as corals are inherently warm-water taxa not commonly associated with seaweed-dominated temperate reefs, these findings are consistent with a net tropicalisation. Our study draws attention to processes other than gradual warming that also influence the trajectory of temperate reefs in a changing ocean.

     

Changes in the composition and structure of coral communities of Mju and Moon islands, Nha Trang Bay, South China Sea

In October 2003 and January 2005, comparative observations were made on the reefs of Mju and Moon islands near the city and port of Nha Trang, which we first investigated in 1981. Appreciable changes due to anthropogenic impact have occurred on the reefs that are the nearest to the city. There was a reduction in substrate cover by reef-building corals, a substitution of dominant scleractinian species, and a decrease in the numbers and diversity of common species of corallobionts. The index of species diversity for scleractinians also decreased. The seaweeds Chnoospora and Halimeda spread into all zones of the reefs. Changes in coral communities on more distant and protected reefs were not so marked.     

Differential thermal tolerance between algae and corals may trigger the proliferation of algae in coral reefs

Marine heatwaves can lead to rapid changes in entire communities, including in the case of shallow coral reefs the potential overgrowth of algae. Here we tested experimentally the differential thermal tolerance between algae and coral species from the Red Sea through the measurement of thermal performance curves and the assessment of thermal limits. Differences across functional groups (algae vs. corals) were apparent for two key thermal performance metrics. First, two reef‐associated algae species (Halimeda tuna and Turbinaria ornata) had higher lethal thermal limits than two coral species (Pocillopora verrucosa and Stylophora pistillata) conferring those species of algae with a clear advantage during heatwaves by surpassing the thermal threshold of coral survival. Second, the coral species had generally greater deactivation energies for net and gross primary production rates compared to the algae species, indicating greater thermal sensitivity in corals once the optimum temperature is exceeded. Our field surveys in the Red Sea reefs before and after the marine heatwave of 2015 show a change in benthic cover mainly in the southern reefs, where there was a decrease in coral cover and a concomitant increase in algae abundance, mainly turf algae. Our laboratory and field observations indicate that a proliferation of algae might be expected on Red Sea coral reefs with future ocean warming.     

Spatial genetic patterns in lagoonal, reef-slope and island populations of the coral Platygyra daedalea in Kenya and Tanzania

Considering the rapid degradation of coral reefs, it is becoming increasingly important to assess factors such as levels of intraspecific genetic diversity and degree of connectivity between populations and reefs. In this study, five DNA microsatellite markers were used to infer migration patterns and levels of genetic diversity in ten populations of the faviid coral Platygyra daedalea along the coast of East Africa. Populations from reef-slopes and offshore islands had significantly greater genetic diversity, measured as expected heterozygosity and allelic richness than those of inshore lagoonal reefs. A combination of F-statistics and individual assignment tests indicated moderate to high levels of gene flow among lagoonal populations, and less migration between lagoonal sites and the reef-slope and island sites. These results suggest that reef-slope and island reefs could be important reservoirs of genetic diversity for this coral species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Coral and sea urchin assemblage structure and interrelationships in Kenyan reef lagoons

Patterns of hard coral and sea urchin assemblage structure (species richness, diversity, and abundance) were studied in Kenyan coral reef lagoons which experienced different types of human resource use. Two protected reefs (Malindi and Watamu Marine National Parks) were protected from fishing and coral collection, but exposed to heavy tourist use. One reef (Mombasa MNP) received protection from fishermen for one year and was exploited for fish and corals prior to protection and was defined as a transitional reef. Three reefs (Vipingo, Kanamai, and Diani) were unprotected and experienced heavy fishing and some coral collection. Protected and unprotected reefs were distinct in terms of their assemblage structure with the transitional reef grouping with unprotected reefs based on relative and absolute abundance of coral genera. Protected reefs had slightly higher (p<0.01) coral cover (23.6 ± 8.3 % ± S.D.) than unprotected reefs (16.7 ± 8.5), but the transitional reef had the highest coral cover (30.8 ± 6.4) which increased by 250% since measured in 1987: largely attributable to a large increase inPorites nigrescens cover. Protected reefs had higher coral species richness and diversity and a greater relative abundance ofAcropora, Montipora andGalaxea than unprotected reefs. The transitional reef had high species richness, but lower diversity due to the high dominance ofPorites. Sea urchins showed the opposite pattern with highest diversity in most unprotected reefs. Coral cover, species richness, and diversity were negatively associated with sea urchin abundance, but the relative abundance ofPorites increased with sea urchin abundance to the point wherePorites composed >90% of the coral cover at sites with the highest sea urchin abundance. Effects of coral overcollection was only likely for the genusAcropora (staghorn corals). A combination of direct and indirect effects of human resource use may reduce diversity, species richness, and abundance of corals while increasing the absolute abundance of sea urchins and the relative cover ofPorites.     

Seabird nutrient subsidies alter patterns of algal abundance and fish biomass on coral reefs following a bleaching event

Cross‐ecosystem nutrient subsidies play a key role in the structure and dynamics of recipient communities, but human activities are disrupting these links. Because nutrient subsidies may also enhance community stability, the effects of losing these inputs may be exacerbated in the face of increasing climate‐related disturbances. Nutrients from seabirds nesting on oceanic islands enhance the productivity and functioning of adjacent coral reefs, but it is unknown whether these subsidies affect the response of coral reefs to mass bleaching events or whether the benefits of these nutrients persist following bleaching. To answer these questions, we surveyed benthic organisms and fishes around islands with seabirds and nearby islands without seabirds due to the presence of invasive rats. Surveys were conducted in the Chagos Archipelago, Indian Ocean, immediately before the 2015–2016 mass bleaching event and, in 2018, two years following the bleaching event. Regardless of the presence of seabirds, relative coral cover declined by 32%. However, there was a post‐bleaching shift in benthic community structure around islands with seabirds, which did not occur around islands with invasive rats, characterized by increases in two types of calcareous algae (crustose coralline algae [CCA] and Halimeda spp.). All feeding groups of fishes were positively affected by seabirds, but only herbivores and piscivores were unaffected by the bleaching event and sustained the greatest difference in biomass between islands with seabirds versus those with invasive rats. By contrast, corallivores and planktivores, both of which are coral‐dependent, experienced the greatest losses following bleaching. Even though seabird nutrients did not enhance community‐wide resistance to bleaching, they may still promote recovery of these reefs through their positive influence on CCA and herbivorous fishes. More broadly, the maintenance of nutrient subsidies, via strategies including eradication of invasive predators, may be important in shaping the response of ecological communities to global climate change.     

Overgrowth and killing of corals by the brown alga Lobophora hederacea (Dictyotales,Phaeophyceae) on healthy reefs in New Caledonia: A new case of the epizoism syndrome

Coral reef degradation is often associated with regime shifts from coral‐ to macroalgal‐dominated reefs. These shifts demonstrate that under certain conditions (e.g. coral mortality, decrease in herbivory, increased nutrients supply) some macroalgae may overgrow corals. The outcome of the competition is dependent on algal aggressiveness and the coral susceptibility. In undisturbed reefs, herbivore grazing is regulating macroalgal cover, thus preventing the latter from overgrowing corals. However, some macroalgae have evolved strategies not only to outcompete corals but also to escape herbivory to some extent, allowing overgrowth of some coral species in undisturbed reefs. Epizoism represents one of those successful strategies, and has been previously documented with red algae, cyanobacteria and Lobophora variegata (Dictyotales, Phaeophyceae). Here we report a new case of epizoism leading to coral mortality, involving a recently described species of Lobophora, L. hederacea, overgrowing the coral Seriatopora caliendrum (Pocilloporidae) in undisturbed reefs in New Caledonia.     

Spatial patterns of parrotfish corallivory in the Caribbean: the importance of coral taxa, density and size

The past few decades have seen an increase in the frequency and intensity of disturbance on coral reefs, resulting in shifts in size and composition of coral populations. These changes have lead to a renewed focus on processes that influence demographic rates in corals, such as corallivory. While previous research indicates selective corallivory among coral taxa, the importance of coral size and the density of coral colonies in influencing corallivory are unknown. We surveyed the size, taxonomy and number of bites by parrotfish per colony of corals and the abundance of three main corallivorous parrotfish (Sparisoma viride, Sparisoma aurofrenatum, Scarus vetula) at multiple spatial scales (reefs within islands: 1-100 km, and between islands: >100 km) within the Bahamas Archipelago. We used a linear mixed model to determine the influence of coral taxa, colony size, colony density, and parrotfish abundance on the intensity of corallivory (bites per m(2) of coral tissue). While the effect of colony density was significant in determining the intensity of corallivory, we found no significant influence of colony size or parrotfish abundance (density, biomass or community structure). Parrotfish bites were most frequently observed on the dominant species of reef building corals (Montastraea annularis, Montastraea faveolata and Porites astreoides), yet our results indicate that when the confounding effects of colony density and size were removed, selective corallivory existed only for the less dominant Porites porites. As changes in disturbance regimes result in the decline of dominant frame-work building corals such as Montastraea spp., the projected success of P. porites on Caribbean reefs through high reproductive output, resistance to disease and rapid growth rates may be attenuated through selective corallivory by parrotfish.     

Holocene uplifted coral reefs in Lanyu and Lutao Islands to the southeast of Taiwan

Lanyu and Lutao Islands to the southeast of Taiwan are located in the northern extension of the Luzon Arc. Crustal deformation of these islands provides a key to understand the collision of the Luzon Arc against Taiwan. To clarify the style and the rate of vertical movement during the Holocene, uplifted coral reefs fringing these two islands were investigated. Living corals were also investigated for comparison with fossil corals. It was found that Isopora palifera lives dominantly in the upper slope of the present-day fringing coral reefs in Lanyu Island at an average depth of 101 ± 46 cm (one standard deviation) below mean sea level. Using I. palifera as an accurate indicator of paleo-sea levels, Holocene relative sea-level changes were reconstructed. Lanyu Island has been uplifted continuously at a rate of 2.0 mm yr⁻¹, at least during the late Holocene from 2,269 cal. yr BP to the present. Lutao Island has been uplifted at an average rate of 1.2 mm yr⁻¹, since at least 5,749 cal. yr BP, although it is unclear whether the uplift was continuous. The present observations, combined with the GPS displacement field and deep crustal structure, suggest that the continuous uplift is related to aseismic slip on the Longitudinal Valley Fault.     

Understanding the murky history of the Coral Triangle: Miocene corals and reef habitats in East Kalimantan (Indonesia)

Studies on ancient coral communities living in marginal conditions, including low light, high turbidity, extreme temperatures, or high nutrients, are important to understand the current structure of reefs and how they could potentially respond to global changes. The main goal of this study was to document the rich and well-preserved fossil coral fauna preserved in Miocene exposures of the Kutai Basin in East Kalimantan, Indonesia. Our collections include almost forty thousand specimens collected from 47 outcrops. Seventy-nine genera and 234 species have been identified. Three different coral assemblages were found corresponding to small patch reefs that developed under the influence of high siliciclastic inputs from the Mahakam Delta. Coral assemblages vary in richness, structure, and composition. Platy coral assemblages were common until the Serravallian (Middle Miocene), while branching coral assemblages became dominant in the Tortonian (Late Miocene). By the late Tortonian massive coral assemblages dominated, similar to modern-style coral framework. Our results suggest that challenging habitats, such as the Miocene turbid habitats of East Kalimantan, might have played an important role during the early diversification of the Coral Triangle by hosting a pool of resilient species more likely to survive the environmental changes that have affected this region since the Cenozoic. Further research that integrates fossil and recent turbid habitats may provide a glimpse into the dynamics and future of coral reefs as “typical” clear-water reefs continue to decline in most regions.     

Impact of cyclones on hard coral and metapopulation structure,connectivity and genetic diversity of coral reef fish

Cyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km²); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.