The threat to coral reefs from more intense cyclones under climate change

Ocean warming under climate change threatens coral reefs directly, through fatal heat stress to corals and indirectly, by boosting the energy of cyclones that cause coral destruction and loss of associated organisms. Although cyclone frequency is unlikely to rise, cyclone intensity is predicted to increase globally, causing more frequent occurrences of the most destructive cyclones with potentially severe consequences for coral reef ecosystems. While increasing heat stress is considered a pervasive risk to coral reefs, quantitative estimates of threats from cyclone intensification are lacking due to limited data on cyclone impacts to inform projections. Here, using extensive data from Australia's Great Barrier Reef (GBR), we show that increases in cyclone intensity predicted for this century are sufficient to greatly accelerate coral reef degradation. Coral losses on the outer GBR were small, localized and offset by gains on undisturbed reefs for more than a decade, despite numerous cyclones and periods of record heat stress, until three unusually intense cyclones over 5 years drove coral cover to record lows over >1500 km. Ecological damage was particularly severe in the central‐southern region where 68% of coral cover was destroyed over >1000 km, forcing record declines in the species richness and abundance of associated fish communities, with many local extirpations. Four years later, recovery of average coral cover was relatively slow and there were further declines in fish species richness and abundance. Slow recovery of community diversity appears likely from such a degraded starting point. Highly unusual characteristics of two of the cyclones, aside from high intensity, inflated the extent of severe ecological damage that would more typically have occurred over 100s of km. Modelling published predictions of future cyclone activity, the likelihood of more intense cyclones within time frames of coral recovery by mid‐century poses a global threat to coral reefs and dependent societies.     

DNA microsatellites in the neon damselfish (Pomacentrus coelestis)

To determine the degree of genetic exchange between populations of the neon damselfish, Pomacentrus coelestis, among different reefs of the Great Barrier Reef, Australia, we characterized seven polymorphic microsatellite loci.     

Regional and local variability in recovery of shallow coral communities: Moorea,French Polynesia and central Great Barrier Reef

Coral communities at Moorea, French Polynesia, and on the Great Barrier Reef (GBR), Australia, were severely depleted by disturbances early in the 1980s. Corals were killed by the predatory starfish Acanthaster planci, by cyclones, and/or by depressed sea level. This study compares benthic community structure and coral population structures on three disturbed reefs (Vaipahu-Moorea; Rib and John Brewer Reefs-GBR) and one undisturbed reef (Davies Reef-GBR) in 1987–89. Moorea barrier reefs had been invaded by tall macrophytes Turbinaria ornata and Sargassum sp., whereas the damaged GBR reefs were colonised by a diverse mixture of short macrophytes, turfs and coralline algae. The disturbed areas had broadly similar patterns of living and dead standing coral, and similar progress in recolonisation, which suggests their structure may converge towards that of undisturbed Davies Reef. Corals occupying denuded areas at Vaipahu, Rib and John Brewer were small (median diameter 5 cm in each case) and sparse (means 4–8 m^-2) compared to longer established corals at Davies Reef (median diameter 9 cm; mean 18 m^-2). At Moorea, damselfish and sea urchins interacted with corals in ways not observed in the GBR reefs. Territories of the damselfish Stegastes nigricans covered much of Moorea's shallow reef top. They had significantly higher diversity and density of post-disturbance corals than areas outside of territories, suggesting that the damselfish exerts some influences on coral community dynamics. Sea urchins on Moorea (Diadema setosum Echinometra mathaei, Echinotrix calamaris) were causing widespread destruction of dead standing coral skeletons. Overall, it appears that the future direction and speed of change in the communities will be explicable more in terms of local than regional processes.     

Dispersal in the spiny damselfish,Acanthochromis polyacanthus,a coral reef fish species without a larval pelagic stage

The spiny damselfish, Acanthochromis polyacanthus, is widely distributed throughout the Indo‐Australian archipelago. However, this species lacks a larval dispersal stage and shows genetic differentiation between populations from closely spaced reefs. To investigate the dispersal strategy of this unique species, we used microsatellite markers to determine genetic relatedness at five dispersal scales: within broods of juveniles, between adults within a collection site (~30 m²), between sites on single reefs, between nearby reefs in a reef cluster, and between reef clusters. We sampled broods of juveniles and adults from seven reefs in the Capricorn‐Bunker and Swain groups of the Great Barrier Reef. We found that extra‐pair mating is rare and juveniles remain with their parents until fledged. Adults from single sites are less related than broods but more related than expected by chance. However, there is no evidence of inbreeding suggesting the existence of assortative mating and/or adult migration. Genetic differences were found between all of the reefs tested except between Heron and Sykes reefs, which are separated only by a 2‐km area of shallow water (less than 10 m). There was a strong correlation between genetic distance, geographical distance and water depth. Apparently, under present‐day conditions spiny damselfish populations are connected only between sites of shallow water, through dispersal of adults over short distances. Assuming that dispersal behaviour has not changed, the broad distribution of A. polyacanthus as a species is likely based on historical colonization patterns when reefs were connected by shallow water at times of lower sea levels.     

Responses of coral and fish assemblages to a severe but short-lived tropical cyclone on the Great Barrier Reef,Australia

Changes in reef assemblages of corals and fishes following a tropical cyclone were assessed using data sets from (1) manta tow surveys of entire reef perimeters and (2) intensive surveys of specific sites, across 11 reefs lying close to the cyclone's track. Only one of the reefs experienced an obvious and immediate decline in mean coral cover (from 24 to 8%) due to the cyclone. The abundance and species richness of adult damselfish assemblages on intensive survey sites at this reef were not affected in the short term (6-8 weeks), despite the removal of 48% of living hard coral. Assemblages of adult fishes showed a similar lack of response at three other reefs where no significant habitat changes had occurred. Eleven to twelve months later, the total abundance of damselfishes had decreased substantially at eight of the sampled reefs, while the abundance of larger mobile fishes remained stable. We infer that the effects on coral assemblages reflect the short duration and orientation of the cyclone, the history of exposure to wave energy (influencing life-form structure and therefore degree of fragility), and the degree of consolidation of the reef matrix. The lack of short-term effects of the cyclone on adult fishes shows that these fishes can endure periods of intense underwater turbulence. The lack of change in damselfish assemblages weeks after loss of coral cover implies that this resource was not limiting adult fish densities. The reasons for widespread decreases in damselfish numbers 11-12 months after the cyclone are unknown.     

Meta-population structure in a coral reef fish demonstrated by genetic data on patterns of migration,extinction and re-colonisation

Background  

Management strategies for coral reefs are dependant on information about the spatial population structure and connectivity of reef organisms. Genetic tools can reveal important information about population structure, however, this information is lacking for many reef species. We used a mitochondrial molecular marker to examine the population genetic structure and the potential for meta-population dynamics in a direct developing coral reef fish using 283 individuals from 15 reefs on the Great Barrier Reef, Australia. We employed a hierarchical sampling design to test genetic models of population structure at multiple geographical scales including among regions, among shelf position and reefs within regions. Predictions from island, isolation-by-distance and meta-population models, including the potential for asymmetric migration, local extinction and patterns of re-colonisation were examined.     

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.     

Temporal clustering of tropical cyclones on the Great Barrier Reef and its ecological importance

Tropical cyclones have been a major cause of reef coral decline during recent decades, including on the Great Barrier Reef (GBR). While cyclones are a natural element of the disturbance regime of coral reefs, the role of temporal clustering has previously been overlooked. Here, we examine the consequences of different types of cyclone temporal distributions (clustered, stochastic or regular) on reef ecosystems. We subdivided the GBR into 14 adjoining regions, each spanning roughly 300 km, and quantified both the rate and clustering of cyclones using dispersion statistics. To interpret the consequences of such cyclone variability for coral reef health, we used a model of observed coral population dynamics. Results showed that clustering occurs on the margins of the cyclone belt, being strongest in the southern reefs and the far northern GBR, which also has the lowest cyclone rate. In the central GBR, where rates were greatest, cyclones had a relatively regular temporal pattern. Modelled dynamics of the dominant coral genus, Acropora, suggest that the long-term average cover might be more than 13 % greater (in absolute cover units) under a clustered cyclone regime compared to stochastic or regular regimes. Thus, not only does cyclone clustering vary significantly along the GBR but such clustering is predicted to have a marked, and management-relevant, impact on the status of coral populations. Additionally, we use our regional clustering and rate results to sample from a library of over 7000 synthetic cyclone tracks for the GBR. This allowed us to provide robust reef-scale maps of annual cyclone frequency and cyclone impacts on Acropora. We conclude that assessments of coral reef vulnerability need to account for both spatial and temporal cyclone distributions.

     

Towards modelling the future risk of cyclone wave damage to the world's coral reefs

Tropical cyclones generate extreme waves that can damage coral reef communities. Recovery typically requires up to a decade, driving the trajectory of coral community structure. Coral reefs have evolved over millennia with cyclones. Increasingly, however, processes of recovery are interrupted and compromised by additional pressures (thermal stress, pollution, diseases, predators). Understanding how cyclones interact with other pressures to threaten coral reefs underpins spatial prioritization of conservation and management interventions. Models that simulate coral responses to cumulative pressures often assume that the worst cyclone wave damage occurs within ~100 km of the track. However, we show major coral loss at exposed sites up to 800 km from a cyclone that was both strong (high sustained wind speeds >=33 m/s) and big (widespread circulation >~300 km), using numerical wave models and field data from northwest Australia. We then calculate the return time of big and strong cyclones, big cyclones of any strength and strong cyclones of any size, for each of 150 coral reef ecoregions using a global data set of past cyclones from 1985 to 2015. For the coral ecoregions that regularly were exposed to cyclones during that time, we find that 75% of them were exposed to at least one cyclone that was both big and strong. Return intervals of big and strong cyclones are already less than 5 years for 13 ecoregions, primarily in the cyclone‐prone NW Pacific, and less than 10 years for an additional 14 ecoregions. We identify ecoregions likely at higher risk in future given projected changes in cyclone activity. Robust quantification of the spatial distribution of likely cyclone wave damage is vital not only for understanding past coral response to pressures, but also for predicting how this may change as the climate continues to warm and the relative frequency of the strongest cyclones rises.     

Cyclone effects on coral reef habitats in New Caledonia (South Pacific)

The impacts of the unusually strong Cyclone Erica (March 2003) on coral reef habitats at a site located on the northwest coast of New Caledonia (South Pacific) were assessed using a 6-year data set (2002–2007). We examined the interannual variations of key variables describing reef habitats (live hard and soft corals, dead corals in place, coral debris, algae and relative proportion of mechanically vulnerable and resistant live hard corals). The cyclone-induced disturbances of habitats differed according to three reef types: patch reefs, barrier reefs far from passes (more than 3 km from the nearest pass) and barrier reefs near passes (less than 3 km from the nearest pass). Short-term mechanical damage was detected on the three-dimensional structure of reef habitats with a notable shift from a community dominated by mechanically vulnerable corals to one dominated by resistant corals on barrier reefs far from passes. The history of habitats and their pre-disturbance characteristics, in link with local hydrodynamics, was found to influence their short-term susceptibility to extreme events such as cyclones. However, the most significant effects appeared in the midterm (within 2 years after the cyclone) as the cover of live hard corals significantly decreased by approximately 45% between 2002 and 2004 on all reef types. The short- and midterm disturbances of coral reef habitats are discussed with regard to published temporal variations in reef fish assemblages, underlining the delayed effects of this cyclonic event on fish as well as benthic habitats. Coral reef habitats and live corals had shown significant patterns of recovery 4 years after the cyclone, followed by similar recovery in fish community, suggesting good resilience in a face of this major natural disturbance in an area under moderate anthropogenic pressure.     

Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution

Remote populations are predicted to be vulnerable owing to their isolation from potential source reefs, and usually low population size and associated increased extinction risk. We investigated genetic diversity, population subdivision and connectivity in the brooding reef coral Seriatopora hystrix at the limits of its Eastern Australian (EA) distribution and three sites in the southern Great Barrier Reef (GBR). Over the approximately 1270 km survey range, high levels of population subdivision were detected (global F_ST = 0.224), with the greatest range in pairwise F_ST values observed among the three southernmost locations: Lord Howe Island, Elizabeth Reef and Middleton Reef. Flinders Reef, located between the GBR and the more southerly offshore reefs, was highly isolated and showed the signature of a recent bottleneck. High pairwise F_ST values and the presence of multiple genetic clusters indicate that EA subtropical coral populations have been historically isolated from each other and the GBR. One putative first-generation migrant was detected from the GBR into the EA subtropics. Occasional long-distance dispersal is supported by changes in species composition at these high-latitude reefs and the occurrence of new species records over the past three decades. While subtropical populations exhibited significantly lower allelic richness than their GBR counterparts, genetic diversity was still moderately high. Furthermore, subtropical populations were not inbred and had a considerable number of private alleles. The results suggest that these high-latitude S. hystrix populations are supplemented by infrequent long-distance migrants from the GBR and may have adequate population sizes to maintain viability and resist severe losses of genetic diversity.     

Fine-scale spatial genetic structure and clonal distribution of the cold-water coral Lophelia pertusa

Determining the spatial genetic structure within and among cold-water coral populations is crucial to understanding population dynamics, assessing the resilience of cold-water coral communities and estimating genetic effects of habitat fragmentation for conservation. The spatial distribution of genetic diversity in natural populations depends on the species’ mode of reproduction, and coral species often have a mixed strategy of sexual and asexual reproduction. We describe the clonal architecture of a cold-water coral reef and the fine-scale population genetic structure (<35 km) of five reef localities in the NE Skagerrak. This study represents the first of this type of analysis from deep waters. We used thirteen microsatellite loci to estimate gene flow and genotypic diversity and to describe the fine-scale spatial distribution of clonal individuals of Lophelia pertusa. Within-population genetic diversity was high in four of the five reef localities. These four reefs constitute a genetic cluster with asymmetric gene flow that indicates metapopulation dynamics. One locality, the Säcken reef, was genetically isolated and depauperate. Asexual reproduction was found to be a highly important mode of reproduction for L. pertusa: 35 genetic individuals were found on the largest reef, with the largest clone covering an area of nearly 300 m².     

Presence of cleaner wrasse increases the recruitment of damselfishes to coral reefs

Mutualisms affect the biodiversity, distribution and abundance of biological communities. However, ecological processes that drive mutualism-related shifts in population structure are often unclear and must be examined to elucidate how complex, multi-species mutualistic networks are formed and structured. In this study, we investigated how the presence of key marine mutualistic partners can drive the organisation of local communities on coral reefs. The cleaner wrasse, Labroides dimidiatus, removes ectoparasites and reduces stress hormones for multiple reef fish species, and their presence on coral reefs increases fish abundance and diversity. Such changes in population structure could be driven by increased recruitment of larval fish at settlement, or by post-settlement processes such as modified levels of migration or predation. We conducted a controlled field experiment to examine the effect of cleaners on recruitment processes of a common group of reef fishes, and showed that small patch reefs (61–285 m²) with cleaner wrasse had higher abundances of damselfish recruits than reefs from which cleaner wrasse had been removed over a 12-year period. However, the presence of cleaner wrasse did not affect species diversity of damselfish recruits. Our study provides evidence of the ecological processes that underpin changes in local population structure in the presence of a key mutualistic partner.     

Wave-induced abiotic stress shapes phenotypic diversity in a coral reef fish across a geographical cline

While morphological variation across geographical clines has been well documented, it is often unclear whether such changes enhance individual performance to local environments. We examined whether the damselfish Acanthochromis polyacanthus display functional changes in swimming phenotype across a 40-km cline in wave-driven water motion on the Great Barrier Reef, Australia. A. polyacanthus populations displayed strong intraspecific variation in swimming morphology and performance that matched local levels of water motion: individuals on reefs subject to high water motion displayed higher aspect-ratio fins and faster swimming speeds than conspecifics on sheltered reefs. Remarkably, intraspecific variation within A. polyacanthus spanned over half the diversity seen among closely related damselfish species from the same region. We find that local selection driven by wave-induced abiotic stress is an overarching ecological mechanism shaping the inter- and intraspecific locomotor diversity of coral reef fishes.     

Population structure and connectivity of the mountainous star coral,Orbicella faveolata,throughout the wider Caribbean region

As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef‐building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well‐mixed throughout the basin (F_ST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large‐scale coral reef connectivity throughout the wider Caribbean.     

Habitat dynamics,marine reserve status,and the decline and recovery of coral reef fish communities

Severe climatic disturbance events often have major impacts on coral reef communities, generating cycles of decline and recovery, and in some extreme cases, community‐level phase shifts from coral‐ to algal‐dominated states. Benthic habitat changes directly affect reef fish communities, with low coral cover usually associated with low fish diversity and abundance. No‐take marine reserves (NTRs) are widely advocated for conserving biodiversity and enhancing the sustainability of exploited fish populations. Numerous studies have documented positive ecological and socio‐economic benefits of NTRs; however, the ability of NTRs to ameliorate the effects of acute disturbances on coral reefs has seldom been investigated. Here, we test these factors by tracking the dynamics of benthic and fish communities, including the important fishery species, coral trout (Plectropomus spp.), over 8 years in both NTRs and fished areas in the Keppel Island group, Great Barrier Reef, Australia. Two major disturbances impacted the reefs during the monitoring period, a coral bleaching event in 2006 and a freshwater flood plume in 2011. Both disturbances generated significant declines in coral cover and habitat complexity, with subsequent declines in fish abundance and diversity, and pronounced shifts in fish assemblage structure. Coral trout density also declined in response to the loss of live coral, however, the approximately 2:1 density ratio between NTRs and fished zones was maintained over time. The only post‐disturbance refuges for coral trout spawning stocks were within the NTRs that escaped the worst effects of the disturbances. Although NTRs had little discernible effect on the temporal dynamics of benthic or fish communities, it was evident that the post‐disturbance refuges for coral trout spawning stocks within some NTRs may be critically important to regional‐scale population persistence and recovery.     

Relationships between habitat structure and fish communities on coral

The influence of habitat structure on reef-fish communities at Bar Reef Marine Sanctuary, Sri Lanka, was investigated. The relationship between habitat characteristics and the distribution and abundance of 135 species of fishes was examined on two reef types: coral and sandstone reefs. Results suggested that the reef-fish communities were strongly influenced by various aspects of reef structure. However, relationships between habitat variables and fish communities structure, varied between the two reef types. Fish species diversity was correlated with a number of habitat variables on the sandstone reefs, although structural complexity seemed to play the dominant role. There were no correlations between habitat structure and fish diversity on the coral reefs. Total abundance was not related to any one habitat parameter on either reef type. However, abundances of some species, families and trophic groups were correlated with habitat features. These specific correlations were commonly related to food or shelter availability. For example, coral feeders were correlated with live coral cover, and pomacentrid species, which used branching corals for protection, showed a significant relationship with the density of Acropora colonies. This shows that a summary statistic such as total abundance may hide important information. Effects of habitat structure on the distribution patterns of the fish communities was further investigated using multi-dimensional scaling ordination (MDS) and the RELATE-procedure. With the MDS ordinations for both habitat and fish-community composition it was possible to show that the multivariate pattern between the two ecological components was clearly correlated.     

Subtle genetic connectivity between Mexican Caribbean and south-western Gulf of Mexico reefs: the case of the bicolor damselfish,Stegastes partitus

Efficient reef management strategies rely on detailed knowledge of biological exchange dynamics. At present, available connectivity information on Mexican Atlantic reefs is scarce, particularly concerning the Veracruz Reef System (VRS), which is located in the south-western Gulf of Mexico. This study used a hierarchically nested sampling design to evaluate the levels of genetic connectivity both within and between the Mexican Caribbean (MC) and VRS reef regions; all of the studied reefs are marine protected areas. Microsatellites were used as genetic markers, and bicolor damselfish (Stegastes partitus) recruits were used as a biological model. The paired genetic differentiation index between regions (Fst _(ENA) = 0.008) was lower than the global index (Fst _(ENA) = 0.027), suggesting that the stronger restrictions to gene flow may be located inside the regions rather than between them. The AMOVA results supported this explanation, as the differences were only non-significant between regions. In the VRS, Santiaguillo reef was associated with low genetic connectivity levels, whilst within the MC region the group formed by Chinchorro Bank and Cozumel exhibited a restriction to gene flow with Puerto Morelos, their northernmost reef. Despite their spatial separation, reefs from different regions (Puerto Morelos and Anegada de Adentro) showed the lowest, albeit significant, genetic difference, meaning that a subtle genetic connectivity exists at the regional scale. The detected composite flow pattern is likely related to self-recruitment and cohesive dispersal processes interacting with current patterns, which may favour genetic connections under specific conditions. The results presented here suggest that coral reef management in the Mexican Atlantic Ocean should consider large scale measures in addition to appropriate local actions to protect reef fish populations.     

Effects of territorial damselfish on an algal-dominated coastal coral reef

Territorial damselfish are important herbivores on coral reefs because they can occupy a large proportion of the substratum and modify the benthic community to promote the cover of food algae. However, on coastal coral reefs damselfish occupy habitats that are often dominated by unpalatable macroalgae. The aim of this study was to examine whether damselfish can maintain distinctive algal assemblages on a coastal reef that is seasonally dominated by Sargassum (Magnetic Island, Great Barrier Reef). Here, three abundant species (Pomacentrus tripunctatus, P. wardi and Stegastes apicalis) occupied up to 60% of the reef substrata. All three species promoted the abundance of food algae in their territories. The magnitudes of the effects varied among reef zones, but patterns were relatively stable over time. Damselfish appear to readily co-exist with large unpalatable macroalgae as they can use it as a substratum for promoting the growth of palatable epiphytes. Damselfish territories represent patches of increased epiphyte load on macroalgae, decreased sediment cover, and enhanced cover of palatable algal turf.     

Spatial and temporal genetic structure of Symbiodinium populations within a common reef‐building coral on the Great Barrier Reef

The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12‐year period including during flood plume–induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70–86% of the total genetic variation. An additional 9–27% of variation was explained by significant differentiation of populations among sites separated by 0.4–13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6–7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site‐wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.