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.     

Geomorphology and Late Quaternary development of Middleton and Elizabeth Reefs

Middleton and Elizabeth Reefs are two mid-latitude, annular reefs within the Lord Howe linear chain of volcanic islands and seamounts in the southwestern Pacific Ocean. Drilling, vibrocoring, seismic profiling, and dating indicate that each has a rim of Holocene reef framework, enclosing a lagoon partly filled by prograding sand sheets composed of fragments of coral, coralline algae, foraminifers, and other skeletal debris. The reefs lie close to the latitudinal limits for coral growth and the reef framework is very porous, dominated by branching rather than massive corals. Coralline algae are the principal binding agent in the upper reef framework. Holocene reef growth began on a foundation of Pleistocene reefal limestone encountered at a depth of 8 m in cores on the windward side of Middleton Reef. Holocene corals became established on this foundation around 6,700 radiocarbon yr B.P., implying little if any lag after inundation of the platform by the post-glacial sea-level rise. Windward reef growth tracked sea-level rise (keep-up mode), and a prominent reef crest was established on both reefs by 5,000 yr B.P. Leeward margins appear to have been characterized by catch-up growth. Development of cays is limited, and has been restricted by the paucity of coarse coralline debris or cemented conglomerate on which islands could become established. The morphology and development of Middleton and Elizabeth Reefs has been similar to that of tropical atolls, although the rate of subsidence appears to have been relatively slow reflecting their position on the margin of the foundered continental crust of the Lord Howe Rise.     

Limited contemporary gene flow and high self‐replenishment drives peripheral isolation in an endemic coral reef fish

Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long‐term persistence of these species following local extinction. This study explored population connectivity in the ecologically‐specialized endemic three‐striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self‐replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self‐replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self‐replenishment (95%), and low contemporary abundance.     

Climate change, genotypic diversity and gene flow in reef-building corals

In the ocean, large‐scale dispersal and replenishment by larvae is a key process underlying biological changes associated with global warming. On tropical reefs, coral bleaching, degradation of habitat and declining adult stocks are also likely to change contemporary patterns of dispersal and gene flow and may lead to range contractions or expansions. On the Great Barrier Reef, where adjacent reefs form a highly interconnected system, we use allozyme surveys of c. 3000 coral colonies to show that populations are genetically diverse, and rates of gene flow for a suite of five species range from modest to high among reefs up to 1200 km apart. In contrast, 700 km further south on Lord Howe Island, genetic diversity is markedly lower and populations are genetically isolated. The virtual absence of long‐distance dispersal of corals to geographically isolated, oceanic reefs renders them extremely vulnerable to global warming, even where local threats are minimal.     

No-take reserves protect coral reefs from predatory starfish

The crown-of-thorns starfish, Acanthaster planci, is a predator of corals that is a major management issue on coral reefs [1]. It occurs throughout the Indo–Pacific and shows boom–bust population dynamics with low background densities and intermittent outbreaks. Three waves of population outbreaks have affected Australia's Great Barrier Reef (GBR) since the 1960s. The waves of outbreaks appear to start 15°S [2] and progress southward through the central GBR (Figure 1A), causing major losses of living coral on many reefs across a large area and dwarfing losses from other disturbances such as storms or coral bleaching over the same period [3]. Humans can potentially influence starfish population dynamics by exploiting predators, though evidence to date is circumstantial. Extensive surveys in the GBR Marine Park (GBRMP) show that protection from fishing affects the frequency of outbreaks: the relative frequency of outbreaks on reefs that were open to fishing was 3.75 times higher than that on no-take reefs in the mid-shelf region of the GBR, where most outbreaks occur, and seven times greater on open reefs if all reefs were included. Although exploited fishes are unlikely to prey on starfish directly, trophic cascades could favour invertebrates that prey on juvenile starfish.     

Recruitment patterns of scleractinian corals in an isolated sub-tropical reef system

The density of recruits of scleractinian corals on settlement plates at Lord Howe Island, a small isolated sub-tropical island 630 km off the Australian coastline, was within the range of values reported for comparable studies on the Great Barrier Reef. However, there was a difference in the relative abundance of taxonomic groups, with recruitment at Lord Howe Island during the summer of 1990/91 dominated by corals from the Family Pocilloporidae, Family Poritidae, and sub-genus Acropora (Isopora) (in order of abundance). By contrast, on the Great Barrier Reef, recruits are generally predominantly species from the Family Acroporidae (other than the Acropora (Isopora) group). Both the recruits and the established coral communities at Lord Howe Island are dominanted by corals which release brooded planulae, as opposed to the pattern of mass-spawning with external fertilisation more typical of Great Barrier Reef corals. I hypothesise that the release of brooded planulae would be advantageous in an isolated reef community because (a) brooded larvae can travel large distances and survive the journey to the isolated reef and/or (b) brooded larvae have a shorter period before they are competent to settle and are therefore more likely to be retained on the parental reef once a population has been established.     

Latitudinal variation in coral communities in eastern Australia: a qualitative biophysical model of factors regulating coral reefs

The processes underlying the distributional limits of both corals and coral reefs can be elucidated by examining coral communities at high latitudes. Coral-dominated communities in eastern Australia cover a latitudinal range of >2,500 km, from the northern Great Barrier Reef (11°S) to South West Rocks (31.5°S). Patterns of coral species richness from 11 locations showed a clear separation between the Great Barrier Reef and subtropical sites, with a further abrupt change at around 31°S. Differences in community structure between the Great Barrier Reef and more southern sites were mainly attributable to higher cover of massive corals, branching Acropora, dead coral and coralline algae on the Great Barrier Reef, and higher cover of macroalgae and bare rock at more southern sites. The absence of some major reef-building taxa (i.e., staghorn Acropora and massive Porites) from most subtropical sites coincided with the loss of reef accretion capacity. Despite high cover of hard corals in communities at up to 31°S, only Lord Howe Island contained areas of reef accretion south of the Great Barrier Reef. Factors that have been hypothesized to account for latitudinal changes in coral community structure include water temperature, aragonite saturation, light availability, currents and larval dispersal, competition between corals and other biota including macroalgae, reduced coral growth rates, and failure of coral reproduction or recruitment. These factors do not operate independently of each other, and they interact in complex ways.     

Predicting the Location and Spatial Extent of Submerged Coral Reef Habitat in the Great Barrier Reef World Heritage Area,Australia

Aim

Coral reef communities occurring in deeper waters have received little research effort compared to their shallow-water counterparts, and even such basic information as their location and extent are currently unknown throughout most of the world. Using the Great Barrier Reef as a case study, habitat suitability modelling is used to predict the distribution of deep-water coral reef communities on the Great Barrier Reef, Australia. We test the effectiveness of a range of geophysical and environmental variables for predicting the location of deep-water coral reef communities on the Great Barrier Reef.

Location

Great Barrier Reef, Australia.

Methods

Maximum entropy modelling is used to identify the spatial extent of two broad communities of habitat-forming megabenthos phototrophs and heterotrophs. Models were generated using combinations of geophysical substrate properties derived from multibeam bathymetry and environmental data derived from Bio-ORACLE, combined with georeferenced occurrence records of mesophotic coral communities from autonomous underwater vehicle, remotely operated vehicle and SCUBA surveys. Model results are used to estimate the total amount of mesophotic coral reef habitat on the GBR.

Results

Our models predict extensive but previously undocumented coral communities occurring both along the continental shelf-edge of the Great Barrier Reef and also on submerged reefs inside the lagoon. Habitat suitability for phototrophs is highest on submerged reefs along the outer-shelf and the deeper flanks of emergent reefs inside the GBR lagoon, while suitability for heterotrophs is highest in the deep waters along the shelf-edge. Models using only geophysical variables consistently outperformed models incorporating environmental data for both phototrophs and heterotrophs.

Main Conclusion

Extensive submerged coral reef communities that are currently undocumented are likely to occur throughout the Great Barrier Reef. High-quality bathymetry data can be used to identify these reefs, which may play an important role in resilience of the GBR ecosystem to climate change.     

Coral growth on three reefs: development of recovery benchmarks using a space for time approach

This 14-year study (1989–2003) develops recovery benchmarks based on a period of very strong coral recovery in Acropora-dominated assemblages on the Great Barrier Reef (GBR) following major setbacks from the predatory sea-star Acanthaster planci in the early 1980s. A space for time approach was used in developing the benchmarks, made possible by the choice of three study reefs (Green Island, Feather Reef and Rib Reef), spread along 3 degrees of latitude (300 km) of the GBR. The sea-star outbreaks progressed north to south, causing death of corals that reached maximum levels in the years 1980 (Green), 1982 (Feather) and 1984 (Rib). The reefs were initially surveyed in 1989, 1990, 1993 and 1994, which represent recovery years 5–14 in the space for time protocol. Benchmark trajectories for coral abundance, colony sizes, coral cover and diversity were plotted against nominal recovery time (years 5–14) and defined as non-linear functions. A single survey of the same three reefs was conducted in 2003, when the reefs were nominally 1, 3 and 5 years into a second recovery period, following further Acanthaster impacts and coincident coral bleaching events around the turn of the century. The 2003 coral cover was marginally above the benchmark trajectory, but colony density (colonies.m⁻²) was an order of magnitude lower than the benchmark, and size structure was biased toward larger colonies that survived the turn of the century disturbances. The under-representation of small size classes in 2003 suggests that mass recruitment of corals had been suppressed, reflecting low regional coral abundance and depression of coral fecundity by recent bleaching events. The marginally higher cover and large colonies of 2003 were thus indicative of a depleted and aging assemblage not yet rejuvenated by a strong cohort of recruits.     

Recovery of the coral Montastrea annularis in the Florida Keys after the 1987 Caribbean “bleaching event”

Many reef-building corals and other cnidarians lost photosynthetic pigments and symbiotic algae (zooxanthellae) during the coral bleaching event in the Caribbean in 1987. The Florida Reef Tract included some of the first documented cases, with widespread bleaching of the massive coral Montastrea annularis beginning in late August. Phototransects at Carysfort Reef showed discoloration of >90% of colonies of this species in March 1988 compared to 0% in July 1986; however no mortality was observed between 1986 and 1988. Samples of corals collected in February and June 1988 had zooxanthellae densities ranging from 0.1 in the most lightly colored corals, to 1.6x10⁶ cells/cm² in the darker corals. Minimum densities increased to 0.5x10⁶ cells/cm² by August 1989. Chlorophyll-a content of zooxanthellae and zooxanthellar mitotic indices were significantly higher in corals with lower densities of zooxanthellae, suggesting that zooxanthellar at low densities may be more nutrientsufficient than those in unbleached corals. Ash-free dry weight of coral tissue was positively correlated with zooxanthellae density at all sample times and was significantly lower in June 1988 compared to August 1989. Proteins and lipids per cm² were significantly higher in August 1989 than in February or June, 1988. Although recovery of zooxanthellae density and coral pigmentation to normal levels may occur in less than one year, regrowth of tissue biomass and energy stores lost during the period of low symbiont densities may take significantly longer.     

Reef location has a greater impact than coral bleaching severity on the microbiome of Pocillopora acuta

Coral Reefs - Coral reefs are increasingly threatened by heat stress events leading to coral bleaching. In 2016, a mass bleaching event affected large parts of the Great Barrier Reef (GBR). Whilst...     

Abundance,diversity, and feeding behavior of coral reef butterflyfishes at Lord Howe Island

Endemic species are assumed to have a high risk of extinction because their restricted geographic range is often associated with low abundance and high ecological specialization. This study examines the abundance of Chaetodon butterflyfishes at Lord Howe Island in the south‐west Pacific, and compares interspecific differences in local abundance to the feeding behavior and geographic range of these species. Contrary to expected correlations between abundance and geographic range, the single most abundant species of butterflyfish was Chaetodon tricinctus, which is endemic to Lord Howe Island and adjacent reefs; densities of C. tricinctus (14.1 ± 2.1 SE fish per 200m²) were >3 times higher than the next most abundant butterflyfish (Chaetodon melannotus), and even more abundant than many other geographically widespread species. Dietary breadth for the five dominant butterflyfishes at Lord Howe Island was weakly and generally negative correlated with abundance. The endemic C. tricinctus was a distinct outlier in this relationship, though our extensive feeding observations suggest some issues with the measurements of dietary breadth for this species. Field observations revealed that all bites taken on benthic substrates by C. tricinctus were from scleractinian corals, but adults rarely, if ever, took bites from the benthos, suggesting that they may be feeding nocturnally and/or using mid‐water prey, such as plankton. Alternatively, the energetic demands of C. tricinctus may be fundamentally different to other coral‐feeding butterflyfishes. Neither dietary specialization nor geographic range accounts for interspecific variation in abundance of coral reef butterflyfishes at Lord Howe Island, while much more work on the foraging behavior and population dynamics of C. tricinctus will be required to understand its’ abundance at this location.     

Assessing loss of coral cover on Australia’s Great Barrier Reef over two decades, with implications for longer-term trends

While coral reefs in many parts of the world are in decline as a direct consequence of human pressures, Australia’s Great Barrier Reef (GBR) is unusual in that direct human pressures are low and the entire system of ~2,900 reefs has been managed as a marine park since the 1980s. In spite of these advantages, standard annual surveys of a large number of reefs showed that from 1986 to 2004, average live coral cover across the GBR declined from 28 to 22%. This overall decline was mainly due to large losses in six (21%) of 29 subregions. Declines in live coral cover on reefs in two inshore subregions coincided with thermal bleaching in 1998, while declines in four mid-self subregions were due to outbreaks of predatory starfish. Otherwise, living coral cover increased in one subregion (3%) and 22 subregions (76%) showed no substantial change. Reefs in the great majority of subregions showed cycles of decline and recovery over the survey period, but with little synchrony among subregions. Two previous studies examined long-term changes in live coral cover on GBR reefs using meta-analyses including historical data from before the mid-1980s. Both found greater rates of loss of coral and recorded a marked decrease in living coral cover on the GBR in 1986, coinciding exactly with the start of large-scale monitoring. We argue that much of the apparent long-term decrease results from combining data from selective, sparse, small-scale studies before 1986 with data from both small-scale studies and large-scale monitoring surveys after that date. The GBR has clearly been changed by human activities and live coral cover has declined overall, but losses of coral in the past 40–50 years have probably been overestimated.     

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.     

Assessing loss of coral cover on the Great Barrier Reef: A response to Hughes et al. (2011)

Hughes et al. (Coral Reefs, 2011, in press) challenge our interpretations of the changes in coral cover observed on the Great Barrier Reef (GBR) between 1986 and 2004 (Sweatman et al. in Coral Reefs 30:521–531, 2011). They question whether we can accurately assign all causes of coral loss; we contend that this makes no difference to the observed changes. They defend the validity of historical data on coral cover from before the start of systematic large-scale monitoring and conclude that coral cover has been declining since at least 1960, but we find no trend in the early data. We remain convinced that combining data collected at different spatial scales (quadrats and transects in the past mixed with more recent whole-reef averages from manta tows) are likely to overestimate decline, because whole-reef averages will very rarely reach the high cover values that can occur at the quadrat scale. Hughes et al. (Coral Reefs, 2011, in press) state that we dismiss runoff as a cause of ecosystem degradation; we defend our interpretations and dispute some of their examples. In summary, we stand by our conclusion that coral cover on the GBR declined in the period 1986–2004 but through localised and unsynchronised changes that included recovery.     

Population genetic and behavioural variation of the two remaining colonies of Providence petrel (<Emphasis Type="Italic">Pterodroma solandri</Emphasis>)

Knowledge of the dispersal capacity of species is crucial to assess their extinction risk, and to establish appropriate monitoring and management strategies. The Providence petrel (Pterodroma solandri) presently breeds only at Lord Howe Island (~32,000 breeding pairs) and Phillip Island-7 km south of Norfolk Island (~20 breeding pairs). A much larger colony previously existed on Norfolk Island (~1,000,000 breeding pairs) but was hunted to extinction in the 18th Century. Differences in time of return to nesting sites are presently observed between the two extant colonies. Information on whether the Phillip Island colony is a relict population from Norfolk Island, or a recent colonization from Lord Howe Island, is essential to assess long-term sustainability and conservation significance of this small colony. Here, we sequenced the mitochondrial cytochrome b gene and 14 nuclear introns, in addition to genotyping 10 microsatellite loci, to investigate connectivity of the two extant P. solandri populations. High gene flow between populations and recent colonization of Phillip Island (95 % HPD 56–200 ya) are inferred, which may delay or prevent the genetic differentiation of these insular populations. These results suggest high plasticity in behaviour in this species and imply limited genetic risks surrounding both the sustainability of the small Phillip Island colony, and a proposal for translocation of Lord Howe Island individuals to re-establish a colony on Norfolk Island.     

Endemic or introduced? Phylogeography of Asparagopsis (Florideophyceae) in Australia reveals multiple introductions and a new mitochondrial lineage

The red seaweed Asparagopsis taxiformis embodies five cryptic mitochondrial lineages (lineage 1–5) introduced worldwide as a consequence of human mediated transport and climate change. We compared globally collected mitochondrial cox2‐3 intergenic spacer sequences with sequences produced from multiple Australian locations and South Korea to identify Asparagopsis lineages and to reveal cryptic introductions. We report A. taxiformis lineage 4 from Cocos (Keeling) Islands, Australia, and the highly invasive Indo‐Pacific Mediterranean lineage 2 from South Korea and Lord Howe Island, Australia. Phylogeographic analysis showed a clear haplotype and geographic separation between western Australian and Great Barrier Reef (GBR) isolates belonging to the recently described lineage 5. The same lineage, however, was characterized by a substantial genetic and geographic break between the majority of Australian specimens and Asparagopsis collections from South Solitary Island, Southern GBR, Lord Howe Island, Kermadec Islands, Norfolk Island, New Caledonia and French Polynesia. The disjunct geographic distribution and sequence divergence between these two groups supports the recognition of a sixth cryptic A. taxiformis mitochondrial lineage. As climatic changes accelerate the relocation of biota and offer novel niches for colonization, periodic surveys for early detection of cryptic invasive seaweeds will be critical in determining whether eradication or effective containment of the aliens are feasible.     

Impacts of a population outbreak of the urchin Tripneustes gratilla amongst Lord Howe Island coral communities

Subtidal reef surveys within the Lord Howe Island Marine Park revealed that populations of the sea urchin Tripneustes gratilla underwent an explosive outbreak in some regions of the park over a 2-year period. This urchin was rare or absent during 2006 surveys at 33 sites studied, but at sites off northern Lord Howe Island in 2008, densities averaged >1.3 m⁻². Dramatic increases in T. gratilla density (exceeding 4 m⁻²) were observed at some sites. We quantify community-level impacts of T. gratilla using ‘before-after’ and ‘control-impact’ data. Zones closed to fishing exhibited similar increases in T. gratilla density to zones open to fishing. Although not previously reported as a keystone species affecting coral habitat, T. gratilla was found to possess an ‘ecosystem engineer’ function. Outbreak sites were characterised by significant declines in cover of foliose algae, including red algae, which decreased from 11.2% in 2006 compared to 2.5% in 2008. Brown foliose algae also declined at sites where T. gratilla outbreaks occurred, averaging 20.4% in 2006 compared to 1.8% in 2008. By contrast, crustose coralline algal cover increased at sites where high T. gratilla densities were observed, from 2.7% in 2006 to an average of 42.6% in 2008. We found no clear indication of impacts on sessile invertebrates or flow-on effects to other levels of the food web, with no significant change in coral cover or densities of mobile invertebrates or fish populations associated with the T. gratilla outbreak.     

Movement in a large predatory fish: coral trout, Plectropomus leopardus (Pisces: Serranidae), on Heron Reef, Australia

 Movement by the larger more mobile species of coral reef fish plays a significant role in determining patterns in abundance and population structure. Fish movement is also relevant to the use and effectiveness of marine reserves in managing fish populations. Coral trout are large piscivorous serranids supporting major fisheries on the Great Barrier Reef (GBR). This study reports on the within-reef movement of the common coral trout, Plectropomus leopardus, at Heron Reef, southern GBR, over a twelve month period, investigated by tagging and underwater tracking. Tracking of coral trout revealed no apparent relationship between the area moved and stage of tide or time of day. However, movement areas were affected by the size of fish: in spring a linear relationship between fish size and area of movement was measured, but in summer the largest (male) fish moved over significantly smaller areas than medium-sized fish. Movement of males may be related to cleaning behaviour and spawning. Fifty nine percent (n=101) of the tagged fish were resighted over periods of 4–5 months, in “home sites” measuring ∼2000 m². Coral trout were not restricted to home sites, but moved on average 2 km along the reef slope; maximum distances of 7–7.5 km were measured. Coral trout appear to range as mobile, opportunistic predators, but also maintain home sites for access to shelter and cleaning stations. Accepted: 1 August 1996     

Impacts and Recovery from Severe Tropical Cyclone Yasi on the Great Barrier Reef

Full recovery of coral reefs from tropical cyclone (TC) damage can take decades, making cyclones a major driver of habitat condition where they occur regularly. Since 1985, 44 TCs generated gale force winds (≥17 metres/second) within the Great Barrier Reef Marine Park (GBRMP). Of the hurricane strength TCs (≥H1—Saffir Simpson scale; ≥ category 3 Australian scale), TC Yasi (February, 2011) was the largest. In the weeks after TC Yasi crossed the GBRMP, participating researchers, managers and rangers assessed the extent and severity of reef damage via 841 Reef Health and Impact Surveys at 70 reefs. Records were scaled into five damage levels representing increasingly widespread colony-level damage (1, 2, 3) and reef structural damage (4, 5). Average damage severity was significantly affected by direction (north vs south of the cyclone track), reef shelf position (mid-shelf vs outer-shelf) and habitat type. More outer-shelf reefs suffered structural damage than mid-shelf reefs within 150 km of the track. Structural damage spanned a greater latitudinal range for mid-shelf reefs than outer-shelf reefs (400 vs 300 km). Structural damage was patchily distributed at all distances, but more so as distance from the track increased. Damage extended much further from the track than during other recent intense cyclones that had smaller circulation sizes. Just over 15% (3,834 km²) of the total reef area of the GBRMP is estimated to have sustained some level of coral damage, with ~4% (949 km²) sustaining a degree of structural damage. TC Yasi likely caused the greatest loss of coral cover on the GBR in a 24-hour period since 1985. Severely impacted reefs have started to recover; coral cover increased an average of 4% between 2011 and 2013 at re-surveyed reefs. The in situ assessment of impacts described here is the largest in scale ever conducted on the Great Barrier Reef following a reef health disturbance.