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As coral reefs endure increasing levels of disturbance, understanding patterns of recovery following disturbance(s) is paramount to assessing the sustainability of these ecosystems. Given the slow dynamics of coral reefs and the increasing frequency of environmental pressures, management strategies focus on understanding recovery patterns to drive efforts and actively promote the recovery of key coral populations. However, the fine spatial scale heterogeneity of coral dynamics challenges our capacity to understand recovery patterns at large spatial scales and guide effective management actions. In this study, we developed a spatio-temporal statistical model to estimate the long-term trajectories of branching, plate and massive corals at fine-spatial scales and predict their recovery patterns at unobserved locations within a reef. We parameterized the model using repeated and georeferenced observations from 783 locations during 16 years at Heron Reef (Great Barrier Reef, Australia). We then developed indicators of recovery that capture the interplay between coral growth and relative decline from disturbance(s) across time, space and growth morphology. Our results reveal that successful recoveries, expressed in terms of probability, are associated with minimum growth rate thresholds of 4.3\% and 6.4\% (absolute growth, y-2) for branching and plate corals in reef locations that were impacted by disturbance(s) at medium-high levels and historically abundant. As a product of the data revolution, predictive maps from statistical models support the development of new indicators that can support the identification of areas of concern to prioritise management intervention. They should be used into larger spatially explicit modelling framework for decision-making in reef conservation and restoration.

In response to the COVID-19 pandemic-induced emergency pivot to online teaching and assessment, an Academic Safety Net was implemented at a regional Australian university to provide academic student support. Bayesian hierarchical models were used to compare student performance between 2019 and 2020. More students withdrew from subjects in 2020, while fewer students remained enrolled but failed. While there was no overall year effect for overall student achievement, exam achievement increased and on-course assessment achievement decreased in 2020. When achievement was analysed according to an assessment task change, a year effect emerged, with the magnitude and direction of the effect dependent on the task changes. The results indicate that the enrolment component of the Academic Safety Net was an effective equity measure that enabled students an extended opportunity to self-withdraw in response to general impacts of the pandemic; while the results component protected the integrity of results awarded during the emergency pivot.

Outbreaks of the corallivorous Crown-of-Thorns Seastar (CoTS) Acanthaster cf. solaris contribute significantly to coral reef loss. Control of outbreaks is hampered because standard monitoring techniques do not detect outbreaks at early (low density) stages, thus preventing early intervention. We previously demonstrated that eDNA monitoring can detect CoTS at intermediate densities. Here, we test whether detection probability can be improved by (i) targeted site selection or collection at specific times and (ii) moving from an average eDNA copy number approach (based on the limit of quantification) to a presence/absence approach (based on the limit of detection). Using a dataset collected over three years and multiple reef sites, we demonstrated that adding water residence age, sea surface level and temperature into generalized linear models explained low amounts of variance of eDNA copy numbers. Site specific CoTS density, by contrast, was a significant predictor for eDNA copy numbers. Bayesian multi-scale occupancy modelling of the presence/absence data demonstrated that the probability of sample capture (θ) on most reefs with intermediate or high CoTS densities was0.8. Thus, confirming CoTS presence on these reefs would only require 2-3 samples. Sample capture decreased with decreasing CoTS density. Collecting ten filters was sufficient to reliably (based on the lower 95 % Credibility Interval) detect CoTS below nominal outbreak levels (3 Ind. ha

Mercury distribution and bioaccumulation in aquatic ecosystems of tropical Australia is poorly characterised. Barramundi (Lates calcarifer), a widespread high-order predator in both fresh and coastal marine waters of the region, fulfils requirements for a bio-indicator of mercury contamination. In a study of the Mary River system of the Northern Territory, total mercury in the muscle tissue of 300 specimens gathered over four years (2013-2017, across both wet and dry seasons) was determined by direct combustion-atomic absorption spectrometry. Source of nutrition and trophic position of barramundi in the food web was also estimated via carbon and nitrogen isotopes (δ

Good water quality is essential to the health of marine ecosystems, yet current metrics used to track water quality in the Great Barrier Reef are not strongly tied to ecological outcomes. There is a need for a better water quality index (WQI). Benthic irradiance, the amount of light reaching the seafloor, is critical for coral and seagrass health and is strongly affected by water quality. It therefore represents a strong candidate for use as a water quality indicator. Here, we introduce a new index based on remote sensing benthic light (bPAR) from ocean color. Resulting bPAR index timeseries, based on the extent to which the observed bPAR fell short of the locally- and seasonally-specific optimum, showed strong spatial and temporal variability, which was consistent with the dynamics that govern changes in water clarity in the Great Barrier Reef. Our new index is ecologically relevant, responsive to changes in light availability and provides a robust metric that may complement current Great Barrier Reef water quality metrics.

Systematic conservation planning requires spatial information on biodiversity. Such information is often unavailable, forcing spatial planning to rely on assumed relationships between species and environmental features. This problem is particularly acute in large, remote marine protected areas that are proliferating rapidly. Here, we use models to predict whether (a) macrobenthic biodiversity across four taxa (gorgonians, soft corals, hard corals, and sponges) with different life histories are congruent within seascape features through regional space; and (b) models generated in an intensively‐sampled area in one region can predict the occurrence of habitat‐forming macrobenthos in neighboring ones. All four taxa studied showed similar habitat preferences, but high variability in distributions among and within features suggesting factors other than simple geomorphology influence these regional biodiversity patterns. Nonetheless, models derived from one region accurately predicted the presence and absence of the same taxa hundreds of kilometers away. This transferability of models of species occurrences has the potential to deliver improved reserve design in data‐deficient regions.

The tegulid gastropod, Rochia nilotica is harvested in small-scale fisheries throughout Southeast Asia and the Pacific Islands, many of which were created from inter-country translocations. This species is found on structurally complex shallow reefs, but its specific habitat requirements have not yet been quantified in order to maximize the success of future translocations and help future-proof the fishery in changing ocean conditions. At 28 sites around Samoa, where the species was introduced in the early 2000s, we measured a suite of habitat variables along transects in which R. nilotica were counted and the shell sizes measured in a parallel study. Boosted regression tree analyses revealed that R. nilotica were most abundant at reef locations that were shallow, with fairly consistent depth, had high coverage of branching coral, low cover of erect macroalgae, low wave exposure and high surface complexity. Smaller individuals were associated with wide reef flats and high cover of branching coral, whereas larger animals occurred in deeper water with high surface complexity. Multivariate analyses showed this species to be a habitat generalist, sharing much of its niche with an endemic herbivorous gastropod, Tectus pyramis. Future stocking programs should focus on sites with habitats optimal for both adults and juveniles. R. nilotica populations are likely to be especially affected by broadscale stressors that result in declines in live coral cover and substratum complexity and increasing coverage of macroalgae on coral reefs.

Coastal areas are under compounding pressures from urbanization, industrialization, infrastructure growth, and aquaculture. There is hence an urgent need for developing solutions for coastal pollution and ecosystem safety. In this work, based on our long-term and multidisciplinary ecosystem monitoring data, we develop tools to translate the observing data into management information to sustainable coastal use and development. From the existing data and experimental studies, we develop approaches to understand key processes and factors controlling coastal ecosystems and to define thresholds and guidelines values of ecological parameters to determine. With focus on marine ecosystem health assessment, we use the integrating data to describe ecosystem condition, its potential trend and the impact of existing pressures. This present study initially focused on the coastal area of the Yellow Sea, in the JIAOZHOU Bay. The technique of the structured research can be applied to other coastal regions as well to understand how these ecosystems respond to local and global pressures.

Quantifying the role of biophysical and anthropogenic drivers of coral reef ecosystem processes can inform management strategies that aim to maintain or restore ecosystem structure and productivity. However, few studies have examined the combined effects of multiple drivers, partitioned their impacts, or established threshold values that may trigger shifts in benthic cover. Inshore fringing reefs of the Great Barrier Reef Marine Park (GBRMP) occur in high-sediment, high-nutrient environments and are under increasing pressure from multiple acute and chronic stressors. Despite world-leading management, including networks of no-take marine reserves, relative declines in hard coral cover of 40–50% have occurred in recent years, with localized but persistent shifts from coral to macroalgal dominance on some reefs. Here we use boosted regression tree analyses to test the relative importance of multiple biophysical drivers on coral and macroalgal cover using a long-term (12–18 yr) data set collected from reefs at four island groups. Coral and macroalgal cover were negatively correlated at all island groups, and particularly when macroalgal cover was above 20%. Although reefs at each island group had different disturbance-and-recovery histories, degree heating weeks (DHW) and routine wave exposure consistently emerged as common drivers of coral and macroalgal cover. In addition, different combinations of sea-surface temperature, nutrient and turbidity parameters, exposure to high turbidity (primary) floodwater, depth, grazing fish density, farming damselfish density, and management zoning variously contributed to changes in coral and macroalgal cover at each island group. Clear threshold values were apparent for multiple drivers including wave exposure, depth, and degree heating weeks for coral cover, and depth, degree heating weeks, chlorophyll a, and cyclone exposure for macroalgal cover, however, all threshold values were variable among island groups. Our findings demonstrate that inshore coral reef communities are typically structured by broadscale climatic perturbations, superimposed upon unique sets of local-scale drivers. Although rapidly escalating climate change impacts are the largest threat to coral reefs of the GBRMP and globally, our findings suggest that proactive management actions that effectively reduce chronic stressors at local scales should contribute to improved reef resistance and recovery potential following acute climatic disturbances.

We thank the staff of WorldFish Center and the Secretariat of the Pacific Community for their administrative support. Helpful comments were given by N. Andrew, J. Bell, W. Nash and S. Uthicke. We thank N. Agudo, P. Blazer, B. Blockmans, J. Le Dreau and M. Simutoga for their helpful assistance. The project was funded by the Australian Centre for International Agricultural Research (ACIAR) through project FIS/1999/025, the 3 provinces of New Caledonia and the government of France.

Climate change threatens coral reefs across the world. Intense bleaching has caused dramatic coral mortality in many tropical regions in recent decades, but less obvious chronic effects of temperature and other stressors can be equally threatening to the long-term persistence of diverse coral-dominated reef systems. Coral reefs persist if coral recovery rates equal or exceed average rates of mortality. While mortality from acute destructive events is often obvious and easy to measure, estimating recovery rates and investigating the factors that influence them requires long-term commitment. Coastal development is increasing in many regions, and sea surface temperatures are also rising. The resulting chronic stresses have predictable, adverse effects on coral recovery, but the lack of consistent long-term data sets has prevented measurement of how much coral recovery rates are actually changing. Using long-term monitoring data from 47 reefs spread over 10 degrees of latitude on Australia's Great Barrier Reef (GBR), we used a modified Gompertz equation to estimate coral recovery rates following disturbance. We compared coral recovery rates in two periods: 7 years before and 7 years after an acute and widespread heat stress event on the GBR in 2002. From 2003 to 2009, there were few acute disturbances in the region, allowing us to attribute the observed shortfall in coral recovery rates to residual effects of acute heat stress plus other chronic stressors. Compared with the period before 2002, the recovery of fast-growing Acroporidae and of "Other" slower growing hard corals slowed after 2002, doubling the time taken for modest levels of recovery. If this persists, recovery times will be increasing at a time when acute disturbances are predicted to become more frequent and intense. Our study supports the need for management actions to protect reefs from locally generated stresses, as well as urgent global action to mitigate climate change.

Predatory fishes are important components of coral-reef ecosystems of the Great Barrier Reef (GBR) through both the ecological functions they perform and their high value to recreational and commercial fisheries, estimated at $30 million in 2014. However, management of GBR predatory fish populations is hampered by a lack of knowledge of their distribution and abundance, aside from that of the highly targeted coral trout (Plectropomus spp. and Variola spp.). Furthermore, there is little information on how these fishes respond to environmental stressors such as coral bleaching, outbreaks of coral-feeding starfishes (Acanthaster planci) and storms, which limits adaptive management of their populations as the frequency or severity of such natural disturbances increases under climate change. Here, we document the distribution and abundance of 48 species of reef-associated predatory fishes and assess their vulnerability to a range of natural disturbances. There were clear differences in predatory fish assemblages across the continental shelf, but many species were widespread, with few species restricted to either inshore or offshore waters. There was weak latitudinal structure with only a few species restricted to either the northern or southern GBR. On the whole, predatory fishes were surprisingly resistant to the effects of disturbance, with few clear changes in abundance or species richness following 66 documented disturbances of varying magnitudes.

Coral reef management is increasingly focused on supporting the resilience of coral communities to increasing and cumulative pressures. The coral index provides a concise summary of coral community resilience that can be efficiently communicated to a range of management and policy stakeholders. We detail the development of the index both as a technical reference for users but also as an example of an approach that could be more generally applied to the reporting of ecosystem resilience. The index is sensitive to acute impacts that are expected when coral communities are exposed to disturbances such as cyclones, bleaching events or crown-of-thorns outbreaks. Importantly, spatial and temporal trends in the index enable the identification of areas and periods of reduced resilience that suggest chronic environmental pressure imposed by runoff. The ability to summarise complex ecological processes into a single index provides an efficient and intuitive tool for the communication of where, when and which pressures are impacting ecosystem resilience.

Water clarity is a key factor for the health of marine ecosystems. The Australian Great Barrier Reef (GBR) is located on a continental shelf, with >35 major seasonal rivers discharging into this 344,000 km2 tropical to subtropical ecosystem. This work investigates how river discharges affect water clarity in different zones along and across the GBR. For each day over 11 years (2002–2013) we calculated ‘photic depth’ as a proxy measure of water clarity (calibrated to be equivalent to Secchi depth), for each 1 km2 pixel from MODIS-Aqua remote sensing data. Long-term and seasonal changes in photic depth were related to the daily discharge volumes of the nearest rivers, after statistically removing the effects of waves and tides on photic depth. The relationships between photic depths and rivers differed across and along the GBR. They typically declined from the coastal to offshore zones, and were strongest in proximity to rivers in agriculturally modified catchments. In most southern inner zones, photic depth declined consistently throughout the 11-year observation period; such long-term trend was not observed offshore nor in the northern regions. Averaged across the GBR, photic depths declined to 47% of local maximum values soon after the onset of river floods, and recovery to 95% of maximum values took on average 6 months (range: 150–260 days). The river effects were strongest at latitude 14.5°–19.0°S, where river loads are high and the continental shelf is narrow. Here, even offshore zones showed a >40% seasonal decline in photic depth, and 17–24% reductions in annual mean photic depth in years with large river nutrients and sediment loads. Our methodology is based on freely available data and tools and may be applied to other shelf systems, providing valuable insights in support of ecosystem management.

Ecosystem health report cards have become increasingly more important tools for communicating environmental state and assessing progress towards management goals. We provide an overview of the major analytical methods underpinning the translation of observed data into robust health indices. In particular, we outline the process of indicator selection, illustrate a variety of index metrics and describe index aggregation with consideration for weighting and the propagation of uncertainty.

The upper canopy of some rain forests in New Caledonia is dominated by single species. These monodominants are commonly secondary species, their dominance not persisting without disturbance. We tested whether dominance is associated with efficient uptake and use of nutrients (N, P and K), comparing between seedlings of monodominants (Nothofagus spp., Arillastrum gummiferum and Cerberiopsis candelabra) and 14 subordinates, grown in a nursery house. We also tested whether this trend applies more broadly to shade-intolerant trees that regenerate episodically (ER species) versus shade-tolerant trees that regenerate continuously (CR species). In the sun treatment, monodominants had higher photosynthetic nutrient-use efficiency and productivity for N and K, and uptake efficiency for N, P and K, than subordinates; ER species had higher photosynthetic nutrient-use efficiency for N, P and K, and uptake efficiency for N and P, than CR species. Uptake efficiency and productivity per nutrient mass were uncorrelated across species, yet Nothofagus spp., A. gummiferum and C. candelabra combined high levels of both traits for N, and Nothofagus spp. and A. gummiferum combined moderate to high levels for P, in sun-grown seedlings. This trait combination may contribute substantially to competitiveness and post-disturbance dominance on these nutrient-poor soils.

Coral-eating Crown-of-Thorns Sea stars (Acanthaster spp.) are major contributors to coral reef loss in the Indo-Pacific region. A release from food limitation of their planktotrophic larvae through enhanced pelagic productivity is one of the main hypothesis explaining population outbreaks (‘nutrient limitation hypothesis’). To improve the understanding of these outbreaks we developed an automated flow- through larvae rearing system that maintained food (microalgae) at set levels over the course of four 15d experiments. This resulted in stable food concentrations in experimental tanks. Increased algae concentrations had a significant positive effect on larval development and size at 10 and 15 days post fertilization (dpf). Larvae densities had no effect at 10 dpf. At 15 dpf greater larvae densities were associated with declines in larvae size. Larval development was slowed under higher larvae densities. Thus, the effects of algae concentration and larvae density were additive at 15 dpf, with larvae under low densities at a given algae concentration being further developed than those under higher densities. The development of a flow-through system gives greater insight into the effect of algae and larvae concentrations on Acanthaster development, and the system can be applied to further test the nutrient-limitation hypothesis for present and future outbreaks.

Obesity is a global epidemic that results in significant morbidity and mortality. Mutations in the melanocortin 4 receptor (MC4R) gene, which codes for a G‐protein‐coupled receptor responsible for postprandial satiety signaling, have been associated with monogenic obesity. The prevalence of obesity is on the increase in South Africa, and it is hypothesized that mutations in MC4R are a contributing factor. The aim of this study was to perform a retrospective assessment of the relationship between allelic variants of MC4R and BMI in a South African study cohort. DNA was isolated from a demographically representative cohort of 297 individuals and the entire MC4R gene sequenced by Sanger sequencing. Eight previously reported MC4R variants were identified in 42 of the 297 (14.1%) study participants. The most frequently observed MC4R alleles were V103I (4.0%), I170V (1.5%), and I198I (1.2%), while the remaining five variants together constituted 1.18%. Five compound heterozygotes were also detected. Although MC4R variants were rare, the majority of variation was observed in individuals of Black African ancestry. No statistically significant associations with BMI were reported. Given that lifestyle interventions have limited success in decreasing obesity, there is an urgent need to perform large‐scale population studies to further elucidate the molecular underpinnings of this disease.

Crustose coralline algae (CCA) are well known for their ability to induce settlement in coral larvae. While their wide distribution spans reefs that differ substantially in temperature regimes, the extent of local adaptation to these regimes and the impact they have on CCA inductive ability are unknown. CCA Porolithon onkodes from Heron (southern) and Lizard (northern) islands on Australia’s Great Barrier Reef (separated by 1181 km) were experimentally exposed to acute or prolonged thermal stress events and their thermal tolerance and recruitment capacity determined. A sudden onset bleaching model was developed to determine the health status of CCA based on the rate of change in the CCA live surface area (LSA). The interaction between location and temperature was significant (F (2,119) = 6.74, p = 0.0017), indicating that thermally driven local adaptation had occurred. The southern population remained healthy after prolonged exposure to 28 °C and exhibited growth compared to the northern population (p = 0.022), with its optimum temperature determined to be slightly below 28 °C. As expected, at the higher temperatures (30 and 32 °C) the Lizard Island population performed better that those from Heron Island, with an optimum temperature of 30 °C. Lizard Island CCA displayed the lowest bleaching rates at 30 °C, while levels consistently increased with temperature in their southern counterparts. The ability of those CCA deemed thermally tolerant (based on LSA) to induce Acropora millepora larval settlement was then assessed. While spatial differences influenced the health and bleaching levels of P. onkodes during prolonged and acute thermal exposure, thermally tolerant fragments, regardless of location, induced similar rates of coral larval settlement. This confirmed that recent thermal history does not influence the ability of CCA to induce settlement of A. millepora larvae.

In a changing ocean, tropical waters can be instructive as to the potential effects of climate induced changes on marine ecosystem structure and function. We describe the relationships between planktonic community respiration (CR), net community production (NCP), gross primary production (GPP), and environmental variables in 14 regions and three ecosystem types (coastal, coral reef, and open sea) from Australia, Papua New Guinea, and Indonesia. The data are compiled from separate studies conducted between 2002 and 2014 with the goal of better parameterizing the metabolic balance in tropical marine waters. Overall, these regions were strongly autotrophic (average GPP:CR ratio: 2.14 ± 0.98), though our dataset of 783 paired measurements did include some oceanic stations where heterotrophy (GPP:CR < 1) was predominant, and some coastal stations that were intermittently heterotrophic. Our statistical analysis suggested that temperature was the most important determinant of CR in coral reef and ocean ecosystems but less so in coastal ecosystems, where chlorophyll concentration was more important. In contrast, chlorophyll and sampling depth were more important in regulating GPP than temperature. The relationships between temperatures and metabolic rates showed that these were ecosystem-dependent, with coastal ecosystems showing less response to temperature than coral reef and open sea sites. The threshold of GPP to achieve metabolic balance fell in a range between 0.715 mmol O2 m−3 d−1 in the Coral Sea to 10.052 mmol O2 m−3 d−1 in mangrove waterways of Hinchinbrook Channel. These data allow regions in and around northern Australia to be ranked in terms of trophic state, ranging from the oligotrophic Scott Reef (GPP:CR = 0.84 ± 0.08) to productive surface waters of the Kimberley coast (GPP:CR = 5.21 ± 0.62). The measurement of pelagic metabolism shows potential as a quantitative tool to monitor the trophic state of coastal waters.

Some species-rich secondary forests in New Caledonia have a monodominant canopy. Here we investigate growth and biomass allocation traits that might explain single-species’ dominance of these post-disturbance stands, and their later decline in the absence of large-scale disturbance. Seedlings of 20 rain-forest trees were grown in two light treatments in a nursery house. In the sun treatment, monodominants grew faster (56.7 ± 1.4 mg g−1 wk−1) than subordinates (40.2 ± 2.6 mg g−1 wk−1). However, some episodically regenerating (ER) subordinates had high growth rates similar to those of monodominants. In the shade treatment, monodominants and subordinates had similar growth rates (33.7 ± 2.6 and 34.0 ± 1.9 mg g−1 wk−1 respectively). Notably, monodominants in both sun and shade treatments had lower root mass fraction (0.29 ± 0.02 and 0.27 ± 0.02 g g−1 respectively) than subordinates (0.39 ± 0.02 and 0.37 ± 0.02 g g−1). Fast growth in sunny conditions is probably imperative for these relatively shade-intolerant ER monodominants. In field conditions, high shoot mass fraction combined with efficient root performance may facilitate faster growth in monodominants competing with other ER species in sunlit sites. Slower growth in shade may contribute to loss of dominance over time in undisturbed forests.

Coral-eating Crown-of-Thorns Sea stars (Acanthaster spp.) are major contributors to coral reef loss in the Indo-Pacific region. A release from food limitation of their planktotrophic larvae through enhanced pelagic productivity is one of the main hypothesis explaining population outbreaks ('nutrient limitation hypothesis'). To improve the understanding of these outbreaks we developed an automated flow- through larvae rearing system that maintained food (microalgae) at set levels over the course of four 15d experiments. This resulted in stable food concentrations in experimental tanks. Increased algae concentrations had a significant positive effect on larval development and size at 10 and 15 days post fertilization (dpf). Larvae densities had no effect at 10 dpf. At 15 dpf greater larvae densities were associated with declines in larvae size. Larval development was slowed under higher larvae densities. Thus, the effects of algae concentration and larvae density were additive at 15 dpf, with larvae under low densities at a given algae concentration being further developed than those under higher densities. The development of a flow-through system gives greater insight into the effect of algae and larvae concentrations on Acanthaster development, and the system can be applied to further test the nutrient-limitation hypothesis for present and future outbreaks.

Knowledge of the time of HIV-1 infection and the multiplicity of viruses that establish HIV-1 infection is crucial for the in-depth analysis of clinical prevention efficacy trial outcomes. Better estimation methods would improve the ability to characterize immunological and genetic sequence correlates of efficacy within preventive efficacy trials of HIV-1 vaccines and monoclonal antibodies. We developed new methods for infection timing and multiplicity estimation using maximum likelihood estimators that shift and scale (calibrate) estimates by fitting true infection times and founder virus multiplicities to a linear regression model with independent variables defined by data on HIV-1 sequences, viral load, diagnostics, and sequence alignment statistics. Using Poisson models of measured mutation counts and phylogenetic trees, we analyzed longitudinal HIV-1 sequence data together with diagnostic and viral load data from the RV217 and CAPRISA 002 acute HIV-1 infection cohort studies. We used leave-one-out cross validation to evaluate the prediction error of these calibrated estimators versus that of existing estimators and found that both infection time and founder multiplicity can be estimated with improved accuracy and precision by calibration. Calibration considerably improved all estimators of time since HIV-1 infection, in terms of reducing bias to near zero and reducing root mean squared error (RMSE) to 5–10 days for sequences collected 1–2 months after infection. The calibration of multiplicity assessments yielded strong improvements with accurate predictions (ROC-AUC above 0.85) in all cases. These results have not yet been validated on external data, and the best-fitting models are likely to be less robust than simpler models to variation in sequencing conditions. For all evaluated models, these results demonstrate the value of calibration for improved estimation of founder multiplicity and of time since HIV-1 infection.

Planktivorous damselfishes (Pomacentridae) are diverse and abundant on the Great Barrier Reef (GBR), are important prey for commercially harvested coral trout (Plectropomus spp.) and their feeding mode plays a central role in transferring energy from the plankton to the reef. However, little is known about their distribution patterns throughout the GBR and how those patterns are influenced by predators and habitat despite increasing pressures on both. Here we quantify the distribution and abundance of GBR planktivorous damselfishes, then examine the role of coral trout and habitat in shaping their assemblages. The assemblage structure of planktivorous damselfishes varied across the continental shelf, yet their total abundances varied sub-regionally, dependent on differences in coral habitat. Latitudinal patterns were relatively weak. Damselfish assemblages generally retained characteristics of their sub-regional setting over 20 years and assemblage degradation was only associated with major coral losses. Damselfish numbers were not negatively influenced by top-down control from coral trout. Instead, numbers of coral trout and damselfishes were both positively associated with coral habitat and each other. Our findings suggest that a complexity of factors and interactions shape reef fish assemblages and reinforce the fundamental importance of coral as the foundation of healthy reef communities.

Recovery of coral reefs after disturbance relies heavily on replenishment through successful larval settlement and their subsequent survival. As part of an integrated study to determine the potential effects of water quality changes on the resilience of inshore coral communities, scleractinian coral settlement was monitored between 2006 and 2012 at 12 reefs within the inshore Great Barrier Reef. Settlement patterns were only analysed for the family Acroporidae, which represented the majority (84%) of settled larvae. Settlement of Acroporidae to terracotta tiles averaged 0.11 cm-2, representing 34 ± 31.01 (mean ± SD) spat per tile, indicating an abundant supply of competent larvae to the study reefs. Settlement was highly variable among reefs and between years. Differences in settlement among locations partly corresponded to the local cover of adult Acroporidae, while substantial reductions in Acroporidae cover caused by tropical cyclones and floods resulted in a clear reduction in settlement. Much of the observed variability remained unexplained, although likely included variability in both connectivity to, and the fecundity of, adult Acroporidae. The responsiveness of settlement patterns to the decline in Acroporidae cover across all four regions indicates the importance of supply and connectivity, and the vulnerability towards region-wide disturbance. High spatial and temporal variability, in addition to the resource-intensive nature of sampling with settlement tiles, highlights the logistical difficulty of determining coral settlement over large spatial and temporal scales.

Pelagic metabolism (community respiration [CR] and net community production [NCP]) were measured in oxygen flux experiments at 14 locations in waters of the Great Barrier Reef (GBR) lagoon between 16uS and 23uS during the dry seasons of 2008 and 2009 and the wet seasons of 2009 and 2010. These were compared to similar experiments conducted in the wet season of 2005 in the far northern GBR (14uS). Seasonality (wet and dry season) was the greatest determinant of respiration rate, with median CR values of 1.85 mmol O2 m23 d21 in the dry season and 2.87 mmol O2 m23 d21 in the wet season. NCP normally ranged up to 9.16 mmol O2 m23 d21, depending on depth and phytoplankton biomass, though an extreme value of 14.96 mmol O2 m23 d21 occurred during flood conditions. Cross-shelf effects had a strong influence on physicochemical variables but weaker effects on both CR and NCP, though both were higher inshore. All but two stations were net autotrophic, with a median ratio of gross primary production:CR of 1.5. Area-specific CR was 72 6 23 standard deviation (SD) mmol O2 m22 d21 in the dry season and 94 6 27 SD mmol O2 m22 d21 in the wet season. Area-specific NCP was lower in the dry season (41 6 33 SD mmol O2 m22 d21) than in the wet season (55 6 54 SD mmol O2 m22 d21). Peaks in area-specific NCP were associated with floods, intrusions of nutrient-rich sub-thermocline Coral Sea water, and localized phytoplankton blooms but otherwise showed few seasonal or spatial trends. Overall, CR in GBR lagoon waters was comparable to rates in oligotrophic oceanic waters, but NCP was more typical of shelf systems.