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Coastal habitats have faced decades of loss caused by urbanization. Global recognition of the ecosystem services that coastal habitats provide has led to an emphasis on cities to adopt nature-based solutions (NBS). However, a broad assessment of urban areas and their potential to conserve remaining coastal habitat has not been undertaken. Here we apply spatial analytics to investigate 5,096 coastal urban areas in tropical and subtropical regions within the distribution of mangroves, tidal flats, seagrass meadows, and coral reefs, and find

The need for efficient and more accurate ways of monitoring threatened ecosystems is becoming increasingly urgent as climate change intensifies. Coral reefs are an example of an ecosystem in crisis, with widespread declines in coral cover and diversity documented over recent decades. Novel molecular approaches such as biomonitoring using environmental DNA (eDNA) from seawater samples show great potential to complement future coral reef monitoring programs, especially when used in combination with conventional methods. However, eDNA metabarcoding studies often rely on public databases (e.g., GenBank) for assigning taxonomy, which generally limits the number of sequences that can be taxonomically identified. The extent to which building reference tissue sequences improves taxonomic resolution has yet to be fully examined. Here, we combined traditional coral reef monitoring data with eDNA assessments derived from seawater collected at the highly diverse Rowley Shoals in Western Australia. Using two ITS2 assays developed to target basal metazoan DNA and a reference database spiked with 70 local coral specimens, we identified 37 genera and 40 species from 56 1 L seawater samples. We identified considerable overlap of taxa with visual survey data and showed that assignment of amplicon sequence variants was significantly improved when “spiking” the taxonomic classifier with curated sequences of locally collected species. Our findings showcase the potential of eDNA metabarcoding for monitoring the biodiversity of reef corals and highlight the importance of custom reference sequence databases for improving taxonomic resolution in metabarcoding studies.

Anthropogenic impacts at isolated and inaccessible reefs are often minimal, offering rare opportunities to observe fish assemblages in a relatively undisturbed state. The remote Rowley Shoals are regarded as one of the healthiest reef systems in the Indian Ocean with demonstrated resilience to natural disturbance, no permanent human population nearby, low visitation rates, and large protected areas where fishing prohibitions are enforced. We used baited remote underwater video systems (BRUVS) to quantify fish assemblages and the relative abundance of regionally fished species within the lagoon, on the slope and in the mesophotic habitat at the Rowley Shoals at three times spanning 14 years and compared abundances of regionally fished species and the length distributions of predatory species to other isolated reefs in the northeast Indian Ocean. Fish assemblage composition and the relative abundance of regionally fished species were remarkably stable through time. We recorded high abundances of regionally fished species relative to other isolated reefs, including globally threatened humphead Maori wrasse (Cheilinus undulatus) and bumphead parrotfish (Bolbometopon muricatum). Length distributions of fish differed among habitats at the Rowley Shoals, suggesting differences in ontogenetic shifts among species. The Cocos (Keeling) Islands typically had larger‐bodied predatory species than at the Rowley Shoals. Differences in geomorphology, lagoonal habitats, and fishing history likely contribute to the differences among remote reefs. Rowley Shoals is a rare example of a reef system demonstrating ecological stability in reef fish assemblages during a time of unprecedented degradation of coral reefs., Fish assemblage composition and the relative abundance of regionally fished species were remarkably stable through time at the Rowley Shoals. We recorded high abundances of regionally fished species relative to other isolated reefs, including globally threatened humphead Maori wrasse (Cheilinus undulatus) and bumphead parrotfish (Bolbometopon muricatum).

Many people and organizations contributed to the success of this project. We are especially grateful to the following Indigenous groups for help with collections on their sea country: the Bardi and Jawi Niimidiman Aboriginal Corporation, the Bardi Jawi Rangers and Traditional Owners (including Damon Pyke, Chris Sampi, Kevin George, Kevin Ejai, Kevin Dougal, Tasha Stumpagee, Phillip McCarthy, Peter Hunter, Zac Ejai, Paul Davey and Trevor Sampi) and the Mayala Aboriginal Corporation and Traditional Owners (especially Sandy, Alec and Janella Isaac). We also respectfully acknowledge the Wunambal Gaambera Aboriginal Corporation, Traditional Owners and Uunguu Rangers, and the Dambimangari Aboriginal Corporation, Traditional Owners and Rangers for collections that were made from their sea country prior to the commencement of the West Australian Marine Science Institute (WAMSI) 1.1.3 project. The authors would like to thank Kathryn Macmahon, Mike Travers, Glenn Moore, Udhi Hernawan, Joseph DiBattista and Richard Evans for contributing with great collaborative spirit to the project. We are also grateful to all WAMSI staff for their assistance, especially Kelly Waples and Stuart Field. Discussions with Liesl Ludgerus and the Marine Park Planning team at the Department of Biodiversity, Conservation and Attractions were invaluable throughout this study. The authors would also like to thanks Bernd Gruber (bioinformatic pipeline development); David Griffin and Rodrigo Garcia (environmental data); Diversity Arrays Technology (SNP marker development and genotyping); Sam Moyle and Fiona Webster (field assistance); Kimberley Marine Research Station staff; and Karen Miller (project development and manuscript review). Inshore fieldwork was funded through WAMSI and the Australian Institute of Marine Science, and Ashmore Reef fieldwork was funded through the Western Australian Museum/Woodside Collection Project. Data were analysed and interpreted with funding support to lead author JU through the Woodside Coral Reef Research Fellowship. ZR, JU and JG acknowledge the support of ARC Linkage Project LP160101508 to explore coral resilience.

At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterizing the mechanisms of coral resilience to climate change. To explore these mechanisms in the reef coral Acropora tenuis , we collected samples from lagoon and reef slope habitats and combined whole-genome sequencing, ITS2 metabarcoding, experimental heat stress, and transcriptomics. Despite high gene flow across the atoll, we identified clear shifts in allele frequencies between habitats at relatively small linked genomic islands. Common garden heat stress assays showed corals from the lagoon to be more resistant to bleaching, and RNA sequencing revealed marked differences in baseline levels of gene expression between habitats. Our results provide new insight into the complex mechanisms of coral resilience to climate change and highlight the potential for spatially varying selection across complex coral reef seascapes to drive pronounced ecological divergence in climate-related traits.

Coral reefs have evolved over millennia to survive disturbances. Yet, in just a few decades chronic local pressures and the climate catastrophe have accelerated so quickly that most coral reefs are now threatened. Rising ocean temperatures and recurrent bleaching pose the biggest threat, affecting even remote and well-managed reefs on global scales. We illustrate how coral bleaching is altering reefs by contrasting the dynamics of adjacent reef systems over more than two decades. Both reef systems sit near the edge of northwest Australia's continental shelf, have escaped chronic local pressures and are regularly affected by tropical storms and cyclones. The Scott reef system has experienced multiple bleaching events, including mass bleaching in 1998 and 2016, from which it is unlikely to fully recover. The Rowley Shoals has maintained a high cover and diversity of corals and has not yet been impacted by mass bleaching. We show how the dynamics of both reef systems were driven by a combination of local environment, exposure to disturbances and coral life history traits, and consider future shifts in community structure with ongoing climate change. We then demonstrate how applying knowledge of community dynamics at local scales can aid management strategies to slow the degradation of coral reefs until carbon emissions and other human impacts are properly managed.

An understanding of larval dispersal and connectivity in corals provides valuable insight into the processes of population maintenance and replenishment and is vital for effective management. Here, we used a genotyping by sequencing approach to explore patterns of genetic connectivity in two species of coral with different reproductive modes (brooding and broadcast spawning) at the Rowley Shoals in northwest Australia. Our data revealed strikingly different patterns of genetic structure in the two species. High levels of genetic subdivision in the brooding coral I. brueggemanni was consistent with extensive self-recruitment and restricted connectivity. In contrast, the broadcast spawning coral A. digitifera formed a single panmictic population with extensive gene flow. Our results highlight the wide variation in metapopulation connectivity that exists among corals and support the well-established link between reproductive mode and population genetic structure in the marine environment.

Western Australia’s coral reefs have largely escaped the chronic pressures affecting other reefs around the world, but are regularly affected by seasonal storms and cyclones, and increasingly by heat stress and coral bleaching. Reef systems north of 18°S have been impacted by heat stress and coral bleaching during strong El Nino phases and those further south during strong La Nina phases. Cumulative heat stress and the extent of bleaching throughout the northern reefs in 2016 were higher than at any other time on record. To assess the changing regime of disturbance to reef systems across Western Australia (WA), we linked their site-specific exposure to damaging waves and heat stress since 1990 with mean changes in coral cover. Since 2010, there has been a noticeable increase in heat stress and coral bleaching across WA. Over half the reef systems have been severely impacted by coral bleaching since 2010, which was further compounded by cyclones at some reefs. For most (75%) reef systems with long-term data (5–26 yrs), mean coral cover is currently at (or near) the lowest on record and a full recovery is unlikely if disturbances continue to intensify with climate change. However, some reefs have not yet experienced severe bleaching and their coral cover has remained relatively stable or increased in recent years. Additionally, within all reef systems the condition of communities and their exposure to disturbances varied spatially. Identifying the communities least susceptible to future disturbances and linking them through networks of protected areas, based on patterns of larval connectivity, are important research and management priorities in coming years while the causes of climate change are addressed.

Time series data are often observed in ecological monitoring. Frequently such data exhibit nonlinear trends over time potentially due to complex relationships between observed and auxiliary variables, and there may also be sudden declines over time due to major disturbances. This poses substantial challenges for modelling such data and also for model-based adaptive monitoring. We propose novel methods for finding adaptive designs for monitoring when historical data show such nonlinear patterns and sudden declines over time. This work is motivated by a coral reef monitoring program that has been established at Scott Reef; a coral reef off the Western coast of Australia. Data collected for monitoring the health of Scott Reef are considered, and semiparametric and interrupted time series modelling approaches are adopted to describe how these data vary over time. New methods are then proposed that enable adaptive monitoring designs to be found based on such modelling approaches. These methods are then applied to find future monitoring designs at Scott Reef and form a set of recommendations for future monitoring. Through applying the proposed methods, it was found that future information gain is expected to be similar across a variety of different sites, suggesting that no particular location needed to be prioritised at Scott Reef for the next monitoring phase. In addition, it was found that omitting some sampling sites/reef locations was possible without substantial loss in expected information gain, depending upon the disturbances that were observed. The resulting adaptive designs are used to provide recommendations for future monitoring in this region, and for reefs where changes to the current monitoring practices are being sought. Furthermore, as the methods used and developed throughout this study are generic in nature, this research has the potential to improve ecological monitoring more broadly where complex data are being collected over time.

Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.

Interactions between oceanic and atmospheric processes within coral reefs can significantly alter local-scale ( 60%) over most of this system; however, the bleaching patterns were not uniform. Little is known about the processes governing thermodynamic variability within atolls, particularly those that are dominated by large amplitude tides. Here, we identify three mechanisms at Scott Reef that alleviated heat stress during the marine heatwave in 2016: (1) the cool wake of a tropical cyclone that induced temperature drops of 1.3 °C over a period of 8 days; (2) air–sea heat fluxes that interacted with the reef morphology during neap tides at one of the atolls to reduce water temperatures by up to 2.9 °C; (3) internal tidal processes that forced deeper and cooler water (up to 2.7 °C) into some sections of the shallow reefs. The latter two processes created localized areas of reduced temperatures that led to lower incidences of coral bleaching for parts of the reef. We predict these processes are likely to occur in other similar tide-dominated reef environments worldwide. Identifying locations where physical processes reduce heat stress will likely be critical for coral reefs in the future, by maintaining communities that can help facilitate local recovery of reefs following bleaching events that are expected to increase in frequency and severity in the coming decades.

Aim To describe, model and assess the relative importance of environmental and climatic factors likely influencing the regional distribution of coral cover and assemblages with contrasting life histories and susceptibilities to bleaching. Location We compiled the first comprehensive empirical dataset for coral communities in the south-eastern Indian Ocean (SEIO), incorporating information from 392 sites along the western coast of Australia and offshore atolls/islands across ~19° of latitude. Methods We assessed hard coral cover and community composition to genus using point-intercept transects or point-count analysis of digital images taken along transects. We explored spatial variation in environmental conditions and in composition of corals with contrasting life histories. After de-trending the temporal patterns, we assessed the relative importance of environmental metrics to coral cover, life histories and bleaching susceptibility using a full subsets model-selection approach with generalized additive mixed models, accounting for both temporal and among site variation. Results The distribution of temperature, light, the frequency of temperature anomalies and tropical cyclones appear to be drivers of coral community structure. Functional diversity of low- to mid-latitude coral communities may convey some resilience to thermal stress, while higher latitude communities dominated by Competitive and Bleaching-Susceptible taxa may lack this functional resilience. These patterns likely reflect varying historical exposure to cyclones and temperature anomalies. Main conclusions As evident in recent years, changing background conditions and regimes of disturbance in coming decades will shift the distribution, functional diversity and resilience of coral reefs throughout the SEIO. The rate and magnitude of environmental change will ultimately determine the future of the tropical reefs and whether the higher latitude reefs provide some refuge from climate change. Our study highlights the need to quantify the distributional properties of key environmental metrics to better understand and predict reef condition through coming decades.

Not enough time for recovery Coral bleaching occurs when stressful conditions result in the expulsion of the algal partner from the coral. Before anthropogenic climate warming, such events were relatively rare, allowing for recovery of the reef between events. Hughes et al. looked at 100 reefs globally and found that the average interval between bleaching events is now less than half what it was before. Such narrow recovery windows do not allow for full recovery. Furthermore, warming events such as El Niño are warmer than previously, as are general ocean conditions. Such changes are likely to make it more and more difficult for reefs to recover between stressful events. Science , this issue p. 80

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.

Este artículo contiene 10 páginas, 5 figuras., Without drastic efforts to reduce carbon emissions and mitigate globalized stressors, tropical coral reefs are in jeopardy. Strategic conservation and management requires identification of the environmental and socioeconomic factors driving the persistence of scleractinian coral assemblages—the foundation species of coral reef ecosystems. Here, we compiled coral abundance data from 2,584 Indo-Pacific reefs to evaluate the influence of 21 climate, social and environmental drivers on the ecology of reef coral assemblages. Higher abundances of framework-building corals were typically associated with: weaker thermal disturbances and longer intervals for potential recovery; slower human population growth; reduced access by human settlements and markets; and less nearby agriculture. We therefore propose a framework of three management strategies (protect, recover or transform) by considering: (1) if reefs were above or below a proposed threshold of >10% cover of the coral taxa important for structural complexity and carbonate production; and (2) reef exposure to severe thermal stress during the 2014–2017 global coral bleaching event. Our findings can guide urgent management efforts for coral reefs, by identifying key threats across multiple scales and strategic policy priorities that might sustain a network of functioning reefs in the Indo-Pacific to avoid ecosystem collapse.

Decision makers are calling for actionable science to protect coastal ecosystems from adverse impacts. Future sea level rise (SLR) is expected to alter the spatial configuration of coastal habitats and their services. Ensuring conservation efforts are in optimal areas can be achieved using systematic conservation planning, yet plans rarely address multiple goals and uncertainties. We developed and applied a novel multi-ecosystem approach for planning the conservation of coastal ecosystems under future SLR scenarios. Decision support tool Marxan was used to determine priority areas that incorporate habitat connectivity, SLR modelling scenarios and feasibility for conservation in urbanised Moreton Bay in Queensland, Australia, as a case-study. We found that planning based on present conditions will not adequately capture conservation priorities for the future, and has associated financial consequences. Priority conservation areas of Moreton Bay are not well aligned with current protected areas (

Coral reefs have been heavily affected by elevated sea-surface temperature (SST) and coral bleaching since the late 1980s; however, until recently coastal reefs of north-western Australia have been relatively unaffected compared to Timor Sea and eastern Australian reefs. We compare SST time series with changes in coral cover spanning a period of up to 36 years to describe temporal and spatial variability in bleaching and associated coral mortality throughout the Pilbara–Ningaloo region. Declines in coral cover ranged from 12.5 to 51.3%, with relative declines ranging from 38 to 92%. Since 2013, coral cover throughout the region has declined to historically low levels at four of five subregions, with impaired recovery occurring at two subregions. Observations are consistent with global trends of repeated severe heat waves, coral bleaching and acute declines in coral cover. Locations within this study region have already experienced multiple coral-bleaching events within a period of less than 5 years. There is a high likelihood that reefs in the western Pilbara and northern Ningaloo regions will experience more frequent marine heatwaves, coral bleaching and mortality events in the future. Action, therefore, needs to be taken now to support the resilience of coral reef ecosystems in the region, which is arguably the most important coral-reef province on Australia’s western coast.

This study investigated the impacts of acidified seawater (pCO2 ~ 900 μatm) and elevated water temperature (+3 °C) on the early life history stages of Acropora spicifera from the subtropical Houtman Abrolhos Islands (28°S) in Western Australia. Settlement rates were unaffected by high temperature (27 °C, ~250 μatm), high pCO2 (24 °C, ~900 μatm), or a combination of both high temperature and high pCO2 treatments (27 °C, ~900 μatm). There were also no significant differences in rates of post-settlement survival after 4 weeks of exposure between any of the treatments, with survival ranging from 60 to 70 % regardless of treatment. Similarly, calcification, as determined by the skeletal weight of recruits, was unaffected by an increase in water temperature under both ambient and high pCO2 conditions. In contrast, high pCO2 significantly reduced early skeletal development, with mean skeletal weight in the high pCO2 and combined treatments reduced by 60 and 48 %, respectively, compared to control weights. Elevated temperature appeared to have a partially mitigative effect on calcification under high pCO2; however, this effect was not significant. Our results show that rates of settlement, post-settlement survival, and calcification in subtropical corals are relatively resilient to increases in temperature. This is in marked contrast to the sensitivity to temperature reported for the majority of tropical larvae and recruits in the literature. The subtropical corals in this study appear able to withstand an increase in temperature of 3 °C above ambient, indicating that they may have a wider thermal tolerance range and may not be adversely affected by initial increases in water temperature from subtropical 24 to 27 °C. However, the reduction in skeletal weight with high pCO2 indicates that early skeletal formation will be highly vulnerable to the changes in ocean pCO2 expected to occur over the twenty-first century, with implications for their longer-term growth and resilience.

The characterization of distance decay in similarity among plant or animal communities both extends ecosystem description and provides insights into formative ecological events and processes. Here, we examine distance decay among coral communities in a common habitat on northwestern Australian reefs, seeking to better understand the roles of disturbance and coral life history strategies in the changing reefscape. In established communities in 1997, when coral cover and generic richness were uniformly high, there was high similarity (~81 %) and negligible distance decay, both within sets of 15 contiguous 50-m transects and among 250-m sites separated by 500 km. Following a 75 % reduction in coral cover and a comparable loss of generic richness to mass bleaching in 1998, similarity declined to ~67 % and there was strong distance decay at

Split spawning in coral populations occurs when gamete maturation and mass spawning are split over two consecutive months. While split spawning has been observed at many reefs, little is known about the frequency and significance of these events. Here we show that split spawning occurred frequently and predictably over a decade at Scott Reef. Split spawning overlays the biannual spawning pattern in the region and occurs when the full moon falls in the first week of the usual spawning month, or the last week of the previous month. Additionally, in split years most species have their main spawning event after a 13-month lunar cycle, in the month following the usual spawning month. Without split spawning, spawn dates would shift by ~10 days each year to occur outside of optimal environmental windows. Our results suggest that split spawning is driven by a disconnect between lunar and seasonal cues, and is analogous with a ‘leap year’ in coral reproduction, realigning spawning dates with favourable conditions for reproduction., Corals usually undergo single mass spawning events, however, occasionally they split reproductive effort across two months. Here, Foster et al. use 10 years of data to determine the drivers and timing of split spawning, showing that these events realign spawning with optimal environmental conditions.

Globally, anthropogenic disturbances are occurring at unprecedented rates and over extensive spatial and temporal scales. Human activities also affect natural disturbances, prompting shifts in their timing and intensities. Thus, there is an urgent need to understand and predict the response of ecosystems to disturbance. In this study, we investigated whether there are general determinants of community response to disturbance across different community types, locations, and disturbance events. We compiled 14 case studies of community response to disturbance from four continents, twelve aquatic and terrestrial ecosystem types, and eight different types of disturbance. We used community compositional differences and species richness to indicate community response. We used mixed-effects modeling to test the relationship between each of these response metrics and four potential explanatory factors: regional species pool size, isolation, number of generations passed, and relative disturbance intensity. We found that compositional similarity was higher between pre- and post-disturbance communities when the disturbed community was connected to adjacent undisturbed habitat. The number of generations that had passed since the disturbance event was a significant, but weak, predictor of community compositional change; two communities were responsible for the observed relationship. We found no significant relationships between the factors we tested and changes in species richness. To our knowledge, this is the first attempt to search for general drivers of community resilience from a diverse set of case studies. The strength of the relationship between compositional change and isolation suggests that it may be informative in resilience research and biodiversity management.

During 2015-2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year. Water quality and fishing pressure had minimal effect on the unprecedented bleaching in 2016, suggesting that local protection of reefs affords little or no resistance to extreme heat. Similarly, past exposure to bleaching in 1998 and 2002 did not lessen the severity of bleaching in 2016. Consequently, immediate global action to curb future warming is essential to secure a future for coral reefs.

The spring and summer of 2010/11 saw an exceptionally strong La Nina push warm waters from Indonesia down the Western Australian coastline, resulting in a host of extraordinary biological oddities including significant bleaching of Western Australian corals. Here, we report a 79–92 % decline in coral cover for a location in the Ningaloo Marine Park where sustained high water temperatures over an 8-month period left just 1–6 % of corals alive. The severity of bleaching provided an opportunity to investigate the resilience of different taxonomic groups and colony size classes to an acute but protracted episode of thermal stress. While the sub-dominant community of massive growth forms fared reasonably well, the dominant Acropora and Montipora assemblages all died, with the exception of the

We utilized a spatial and temporal analyses of genetic structure, supplemented with ecological and oceanographic analysis, to assess patterns of population connectivity in a coral reef fish Chromis margaritifer among the unique and remote atolls in the eastern Indian Ocean. A subtle, but significant genetic discontinuity at 10 microsatellite DNA loci was detected between atoll systems corresponding with a low (≤ 1%) probability of advection across the hundreds of kilometers of open ocean that separates them. Thus, although genetic connections between systems are likely maintained by occasional long-distance dispersal of C. margaritifer larvae, ecological population connectivity at this spatial scale appears to be restricted. Further, within one of these atoll systems, significant spatial differentiation among samples was accompanied by a lack of temporal pairwise differentiation between recruit and adult samples, indicating that restrictions to connectivity also occur at a local scale (tens of kilometers). In contrast, a signal of panmixia was detected at the other atoll system studied. Lastly, greater relatedness and reduced genetic diversity within recruit samples was associated with relatively large differences among them, indicating the presence of sweepstakes reproduction whereby a small proportion of adults contributes to recruitment in the next generation. These results are congruent with earlier work on hard corals, suggesting that local production of larvae drives population replenishment in these atoll systems for a range of coral reef species.

In 2017, the Australian Institute of Marine Science and its partners commenced the North West Shoals to Shore Research Program. The program is designed to address significant scientific and environmental knowledge gaps pertinent to the management of the offshore petroleum industry, a key stakeholder in this ecologically and commercially important region of Australia. The program comprises four themes. 1. Marine noise monitoring and impacts: includes two seismic source (2600 cubic inch air-gun array) exposure experiments have been conducted to investigate selected responses by demersal fishes and pearl oysters across different spatial and temporal scales. 2. Seabed habitats and demersal biodiversity: seeks to understand the physical and biological characteristics of the ancient coastline key ecological feature around the 125 m depth contour and pearl oyster habitats offshore from Eighty Mile Beach. The work examines the ecological processes that maintain benthic communities on both ancient and contemporary coastlines 3. Protected and iconic species movement, distribution and threats: uses innovative sampling techniques to confirm biologically important areas for pygmy blue whales, hawksbill and green turtles. This will assist the quantification and mitigation of the risks vessel movements, industrial infrastructure and activities pose to marine megafauna on the Northwest Shelf. 4. Spatial dynamics of isolated coral reef atolls: develops a habitat model and adaptive monitoring program that informs the future condition of these remote coral reef atolls. Significant progress has been made by the program in 2018, including the development of innovative and technical approaches to sampling.

Effective environmental management requires monitoring programmes that provide specific links between changes in environmental conditions and ecosystem health. This article reviews the suitability of a range of bioindicators for use in monitoring programmes that link changes in water quality to changes in the condition of coral-reef ecosystems. From the literature, 21 candidate bioindicators were identified, whose responses to changes in water quality varied spatially and temporally; responses ranged from rapid (hours) changes within individual corals to long-term (years) changes in community composition. From this list, the most suitable bioindicators were identified by determining whether responses were (i) specific, (ii) monotonic, (iii) variable, (iv) practical and (v) ecologically relevant to management goals. For long-term monitoring programmes that aim to quantify the effects of chronic changes in water quality, 11 bioindicators were selected: symbiont photophysiology, colony brightness, tissue thickness and surface rugosity of massive corals, skeletal elemental and isotopic composition, abundance of macro-bioeroders, micro- and meiobenthic organisms such as foraminifera, coral recruitment, macroalgal cover, taxonomic richness of corals and the maximal depth of coral-reef development. For short-term monitoring programmes, or environmental impact assessments that aim to quantify the effects of acute changes in water quality, a subset of seven of these bioindicators were selected, including partial mortality. Their choice will depend on the specific objectives and the timeframe available for each monitoring programme. An assessment framework is presented to assist in the selection of bioindicators to quantify the effects of changing water quality on coral-reef ecosystems.

Some of the most important demographic parameters underlying the resilience of coral communities are determined by their patterns of reproduction. In this study, a variety of methods were used to investigate the patterns of spawning, larval development and dispersal for scleractinian corals at an isolated reef system off northwestern Australia. Two distinct periods of gamete maturation and multi-specific spawning occurred each year, during Spring and Autumn, in contrast to the single season of mass spawning described on most other reefs around Australia. The subsequent rates of embryogenesis and larval development were among the fastest described for corals, with pre-competency periods of approximately 3 days. Within 3 days of spawning, slicks of spawn and current drifters had dispersed up to 5 km, and up to 10 km after 6 days, while the times taken for drifters to travel between adjacent (>240 km) reef systems were similar to or greater than the upper competency periods of most coral larvae. Thus, under these conditions, the entire reef system, and to some extent the reefs within the system, may largely be self-seeded; rates of immigration from other systems are probably insufficient to rapidly increase the recovery of communities within years of a major disturbance. These results have implications for the management of isolated reef systems, highlighting the need to minimize local stressors and maximize community resilience to the increasing scale of disturbance and habitat fragmentation.

Coral reefs are in decline worldwide, and marine reserve networks have been advocated as a powerful management tool for maximizing the resilience of coral communities to an increasing variety, number, and severity of disturbances. However, the effective design of reserves must account for the spatial scales of larval dispersal that affect the demography of communities over ecological time frames. Ecologically relevant distances of dispersal were inferred from DNA microsatellite data in a broadcast-spawning (Acropora tenuis) and a brooding (Seriatopora hystrix) coral at isolated reef systems off northwest Australia. Congruent with expectations based on life histories, levels of genetic subdivision among populations were markedly higher in the brooder than in the broadcast spawner. Additionally, significant subdivision for both species between systems (>100 km), and between (>10 km) or within reefs (

A modified drop net (area = 19.3 m2) was constructed to enhance the collection of fish from within complex freshwater habitats. The net was evaluated in three pools located within the Pilbara region of north Western Australia. The net's efficiency was determined by comparison with gillnetting and beach seining; accuracy of the net was investigated using the toxicant rotenone. In terms of efficiency, the modified drop net and beach seine generated similar descriptions of the fish community (relative abundance, species richness, ordination of a species–abundance matrix); panel gill nets collected a diminished subset of the community. Efficiency of the drop net remained relatively constant among pools, whereas the seine became increasingly easy to use as habitat complexity decreased. In terms of accuracy, the drop net produced estimates of total fish abundance similar to those obtained by use of rotenone and adequately depicted site-related differences in fish community structure (multivariate ordin...

On reefs around Australia, coral mass spawning typically occurs during the austral spring (October/November) on the east coast, and during autumn (March/April) on the west coast. However, to investigate the incidence of a secondary spawning event in spring on the west coast, the reproductive state of corals was assessed on two reefs. The results indicated that of the 29 species of Acropora investigated, multiple colonies of 11 species spawned in late spring or in early summer, in contrast to previous reports of spawning during autumn. Additionally, of four species that were followed through time at one reef, two spawned in both spring and autumn, however, individual colonies had only one gametogenic cycle. Within a single site, conspecific colonies were reproductively isolated and may not interbreed, potentially representing the initial stage of sympatric speciation in these populations.

As a result of climate change, sea-water temperatures around the world are expected to increase, potentially causing more frequent and severe episodes of coral bleaching. In this study, the impact of elevated water temperatures at an isolated system of reefs was assessed by quantifying the changes in benthic communities over almost 10 years. Mass-coral bleaching in 1998 dramatically altered the community structure of the reefs, including a >80% relative decrease in the cover of hard and soft corals and a twofold increase in the cover of algae, but which did not include macroalgae. The magnitude of the impact varied among the different sites according to their initial cover and community structure, largely due to the differing susceptibilities of the dominant groups of hard corals. Subsequent increase in the cover of these groups varied according to their life history traits, such as modes of reproduction and rates of growth. Additionally, the increase in cover was strongly correlated with the magnitude of the impact at the different sites, suggesting that recovery was driven by processes acting over local scales. Six years after the bleaching, the hard corals had returned to approximately 40% of their pre-bleaching cover, but there was little change in the cover of soft corals, and the structure of most hard coral communities remained very different to that prior to the bleaching. These data provides insights into the degree to which coral communities are resilient to catastrophic disturbances, when they are isolated from other reef systems but not exposed to some of the chronic stressors affecting many reefs around the world.

Understanding the pattern of connectivity among populations is crucial for the development of realistic and spatially explicit population models in marine systems. Here we analysed variation at eight microsatellite loci to assess the genetic structure and to infer patterns of larval dispersal for a brooding coral, Seriatopora hystrix, at an isolated system of reefs in northern Western Australia. Spatial autocorrelation analyses show that populations are locally subdivided, and that the majority of larvae recruit to within 100 m of their natal colony. Further, a combination of F- and R- statistics showed significant differentiation at larger spatial scales (2-60 km) between sites, and this pattern was clearly not associated with distance. However, Bayesian analysis demonstrated that recruitment has been supplemented by less frequent but recent input of larvae from outside the local area; 2-6% of colonies were excluded from the site at which they were sampled. Individual assignments of these migrants to the most likely populations suggest that the majority of migrants were produced at the only site that was not decimated by a recent and catastrophic coral bleaching event. Furthermore, the only site that recovered to prebleaching levels received most of these immigrants. We conclude that the genetic structure of this brooding coral reflects its highly opportunistic life history, in which prolific, philopatric recruitment is occasionally supplemented by exogenously produced larvae.

In 2017, the Australian Institute of Marine Science and its partners commenced the North West Shoals to Shore Research Program. The program is designed to address significant scientific and environmental knowledge gaps pertinent to the management of the offshore petroleum industry, a key stakeholder in this ecologically and commercially important region of Australia. The program comprises four themes. 1. Marine noise monitoring and impacts: includes two seismic source (2600 cubic inch air-gun array) exposure experiments have been conducted to investigate selected responses by demersal fishes and pearl oysters across different spatial and temporal scales. 2. Seabed habitats and demersal biodiversity: seeks to understand the physical and biological characteristics of the ancient coastline key ecological feature around the 125 m depth contour and pearl oyster habitats offshore from Eighty Mile Beach. The work examines the ecological processes that maintain benthic communities on both ancient and contemporary coastlines 3. Protected and iconic species movement, distribution and threats: uses innovative sampling techniques to confirm biologically important areas for pygmy blue whales, hawksbill and green turtles. This will assist the quantification and mitigation of the risks vessel movements, industrial infrastructure and activities pose to marine megafauna on the Northwest Shelf. 4. Spatial dynamics of isolated coral reef atolls: develops a habitat model and adaptive monitoring program that informs the future condition of these remote coral reef atolls. Significant progress has been made by the program in 2018, including the development of innovative and technical approaches to sampling.

The contribution of asexual versus sexual recruitment to populations of the mushroom coral Fungia fungites was investigated at 2 sites with contrasting sediment regimes, located 5 km apart in the Dampier Archipelago (Western Australia). One site was exposed to high levels of chronic sedimentation, and many of its F. fungites polyps were asexual buds attached to dead parent polyps. A total of 95 buds were sampled from 26 parent skeletons; all buds on each parent were of the same genotype. The second site received less than half the sediment load, and the F. fungites polyps there were not observed to produce asexual buds. I hypothesised that asexual and sexual recruitment would contribute disproportionately to the maintenance of the high- and low-sediment sites respectively. However, electrophoretic analysis of 7 polymorphic loci indicated that sexual recruitment was responsible for the majority of adults in a random sample (n = 120) of polyps from each site. All polyps sampled at the low-sediment site had unique 7 locus genotypes. Between 10 and 30% of the polyps at the sediment-affected site were derived asexually, but all were in juvenile size classes, usually as replicate buds attached to a single parent. No adult polyps shared the same genotype, despite evidence that rarely, some asexual recruits may survive to adult size. Patterns of sexual recruitment underlying both populations were characterised by major heterozygote deficiencies and considerable inbreeding (F IS = 0.571 ± 0.018 SE). Most genetic differentiation occurred between locations within sites (F ST = 0.080) rather that among sites (F ST = 0.022). Dispersal of gametes and larvae appear to be highly localised.

Laboratory and field experiments were used to determine whether high (≃100 mg l−1), low (≃50 mg l−1) and control (≃0 mg l−1) levels of suspended sediment affected fertilisation, larval survival, and larval settlement in the scleractinian coral Acropora digitifera (Dana, 1846). Both high- and low-sediment treatments significantly decreased fertilisation, but post-fertilisation embryonic development was not inhibited by suspended sediments. Larval survival and larval settlement were significantly reduced in high- and low-sediment treatments. No difference was found between high- and low-sediment treatments in any of the three post-spawning processes investigated, suggesting that they are susceptible to sediment concentrations which are not exceptionally high even under natural conditions (>50 mg l−1). The introduction of an additional stress in the form of high levels of suspended sediments coupled with naturally high variability in recruitment may have a considerable effect on the successful supply and settlement of coral larvae to a reef. Given that many coral communities are open reproductive systems, the consequences of disturbance events are not likely to be restricted to the impact area. Recruitment to a population may be reduced significantly in the presence of high levels of suspended sediments because of effects on larval survival and settlement. Recruitment of larvae to adjacent populations may also be affected due to a decreased fertilisation success and potential increases in mortality of larvae passing through the affected site.

Reef Repair Coral reefs suffer mass mortality because of coral bleaching, disease, and tropical storms, but we know much more about when, where, and how rapidly these ecosystems have collapsed than we do about their recovery. Gilmour et al. (p. 69 ; see the Perspective by Polidoro and Carpenter ) studied a highly isolated coral reef before and after a climate-induced mass mortality event that killed 70 to 90% of the reef corals. The initial recovery of coral cover involved growth and survival of remnant colonies, which was followed by increases in larval recruitment. Thus, in the absence of chronic disturbance, even isolated reefs can recover from catastrophic disturbance.

Coral spawning on the oceanic reef systems of north-western Australia was recently discovered during autumn and spring, but the degree to which species and particularly colonies participated in one or both of these spawnings was unknown. At the largest of the oceanic reef systems, the participation by colonies in the two discrete spawning events was investigated over three years in 13 species of Acropora corals (n = 1,855 colonies). Seven species spawned during both seasons; five only in autumn and one only in spring. The majority of tagged colonies (n = 218) spawned once a year in the same season, but five colonies from three species spawned during spring and autumn during a single year. Reproductive seasonality was not influenced by spatial variation in habitat conditions, or by Symbiodinium partners in the biannual spawner Acropora tenuis. Colonies of A. tenuis spawning during different seasons separated into two distinct yet cryptic groups, in a bayesian clustering analysis based on multiple microsatellite markers. These groups were associated with a major genetic divergence (G"ST = 0.469), despite evidence of mixed ancestry in a small proportion of individuals. Our results confirm that temporal reproductive isolation is a common feature of Acropora populations at Scott Reef and indicate that spawning season is a genetically determined trait in at least A. tenuis. This reproductive isolation may be punctuated occasionally by interbreeding between genetic groups following favourable environmental conditions, when autumn spawners undergo a second annual gametogenic cycle and spawn during spring.

We utilized a spatial and temporal analyses of genetic structure, supplemented with ecological and oceanographic analysis, to assess patterns of population connectivity in a coral reef fish Chromis margaritifer among the unique and remote atolls in the eastern Indian Ocean. A subtle, but significant genetic discontinuity at 10 microsatellite DNA loci was detected between atoll systems corresponding with a low (≤ 1%) probability of advection across the hundreds of kilometers of open ocean that separates them. Thus, although genetic connections between systems are likely maintained by occasional long-distance dispersal of C. margaritifer larvae, ecological population connectivity at this spatial scale appears to be restricted. Further, within one of these atoll systems, significant spatial differentiation among samples was accompanied by a lack of temporal pairwise differentiation between recruit and adult samples, indicating that restrictions to connectivity also occur at a local scale (tens of kilometers). In contrast, a signal of panmixia was detected at the other atoll system studied. Lastly, greater relatedness and reduced genetic diversity within recruit samples was associated with relatively large differences among them, indicating the presence of sweepstakes reproduction whereby a small proportion of adults contributes to recruitment in the next generation. These results are congruent with earlier work on hard corals, suggesting that local production of larvae drives population replenishment in these atoll systems for a range of coral reef species.

Inshore coral reefs adjacent to the wet tropics in North Queensland, Australia, are regularly exposed to flood plumes from coastal river systems. Changes in the nature of these plumes have been linked to the declining health of coral reefs in the region. The effect of flood plumes on the health of inshore corals was investigated by quantifying aspects of the demography of populations of corymbose and digitate Acropora at three groups of Island reefs along a gradient of exposure and decreasing water quality (High Island >Frankland’s >Fitzroy). The size-structures of colonies, the rates of sexual recruitment, and the growth and survival of juveniles, all varied among the Island reefs. Juvenile and adult sized colonies were far more abundant at the Fitzroy Island reefs, than at the High or Frankland Island reefs that were more exposed to flood plumes. Additionally, there were up to eight times as many sexual recruits at the Fitzroy Island reefs, compared with the High Island reefs. However, the rates of growth and survival of the juvenile sized corals at the Fitzroy Island reefs were lower than at the more exposed reefs. The comparatively low abundance of adult corals at the exposed reefs is most likely due to their histories of disturbance from crown-of-thorns and coral bleaching, but the lack of subsequent recovery due to their low levels of larval recruitment. If a stock-recruitment relationship is typical for these groups of reefs, then the low rates of recruitment may be linked to the low density of adult colonies. Alternately, direct or indirect effects of chronic exposure to poor water quality may have resulted in less suitable substrata for larval settlement. We discuss these results and provide examples of how information about population structure and dynamics can be used in simple matrix models to quantify the current and future health of populations of corals under various scenarios.

Changes in the size-structure of populations of the mushroom coral Fungia fungites were quantified at two reefs during four annual surveys. Exposure to disturbance was predicted to affect the size and frequency of life history stages of polyps at each reef and their variability through time. The Mainland reef experienced frequent and intense disturbances, primarily as exposure to cyclones and substantial sedimentation, which were comparatively absent from the East Lewis reef. Disturbance to the Mainland reef was evident in the smaller size of polyps, and the many parent polyps, asexual buds, and polyp skeletons, which were all absent from the East Lewis reef. Over three years, the number and area cover of polyps at the Mainland reef decreased to 9% and 3% of their initial values respectively, compared with 73% and 36% at East Lewis. The size-structure of polyps at East Lewis remained comparatively stable; whereas, the abundance of all life history stages at the Mainland reef had high but variable rates of decline each year. Changes in the size-structure of polyps at the Mainland reef indicated it was exposed to levels of disturbance that it had not experienced, and would not recover from, for many years.

Monitoring changes in coral cover and composition through space and time can provide insights to reef health and assist the focus of management and conservation efforts. We used a meta-analytical approach to assess coral cover data across latitudes 10-35°S along the west Australian coast, including 25 years of data from the Ningaloo region. Current estimates of coral cover ranged between 3 and 44% in coral habitats. Coral communities in the northern regions were dominated by corals from the families Acroporidae and Poritidae, which became less common at higher latitudes. At Ningaloo Reef coral cover has remained relatively stable through time (∼28%), although north-eastern and southern areas have experienced significant declines in overall cover. These declines are likely related to periodic disturbances such as cyclones and thermal anomalies, which were particularly noticeable around 1998/1999 and 2010/2011. Linear mixed effects models (LME) suggest latitude explains 10% of the deviance in coral cover through time at Ningaloo. Acroporidae has decreased in abundance relative to other common families at Ningaloo in the south, which might be related to persistence of more thermally and mechanically tolerant families. We identify regions where quantitative time-series data on coral cover and composition are lacking, particularly in north-western Australia. Standardising routine monitoring methods used by management and research agencies at these, and other locations, would allow a more robust assessment of coral condition and a better basis for conservation of coral reefs.

Background Globally, coral bleaching has been responsible for a significant decline in both coral cover and diversity over the past two decades. During the summer of 2010–11, anomalous large-scale ocean warming induced unprecedented levels of coral bleaching accompanied by substantial storminess across more than 12° of latitude and 1200 kilometers of coastline in Western Australia (WA). Methodology/Principal Findings Extreme La-Nina conditions caused extensive warming of waters and drove considerable storminess and cyclonic activity across WA from October 2010 to May 2011. Satellite-derived sea surface temperature measurements recorded anomalies of up to 5°C above long-term averages. Benthic surveys quantified the extent of bleaching at 10 locations across four regions from tropical to temperate waters. Bleaching was recorded in all locations across regions and ranged between 17% (±5.5) in the temperate Perth region, to 95% (±3.5) in the Exmouth Gulf of the tropical Ningaloo region. Coincident with high levels of bleaching, three cyclones passed in close proximity to study locations around the time of peak temperatures. Follow-up surveys revealed spatial heterogeneity in coral cover change with four of ten locations recording significant loss of coral cover. Relative decreases ranged between 22%–83.9% of total coral cover, with the greatest losses in the Exmouth Gulf. Conclusions/Significance The anomalous thermal stress of 2010–11 induced mass bleaching of corals along central and southern WA coral reefs. Significant coral bleaching was observed at multiple locations across the tropical-temperate divide spanning more than 1200 km of coastline. Resultant spatially patchy loss of coral cover under widespread and high levels of bleaching and cyclonic activity, suggests a degree of resilience for WA coral communities. However, the spatial extent of bleaching casts some doubt over hypotheses suggesting that future impacts to coral reefs under forecast warming regimes may in part be mitigated by southern thermal refugia.

Field experiments investigated the effect of acute sedimentation on polyp injury, mortality and bud production in the mushroom coral, Fungia fungites (Linnaeus, 1758). Small (3-5 cm), medium (8-12 cm) and large (15-20 cm) polyps were covered with a layer of sediment in low (2 mm), medium (5 mm) and high (10 mm) treatments, every two days for 20 days. Injury decreased with polyp size, and increased with the amount and duration of sediment addition. Only medium and large polyps briefly (