Influence of life history variation and habitat on mercury bioaccumulation in a high-order predatory fish in tropical Australia.

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 (δ13C and δ15N), respectively, in tissue by stable isotope mass spectrometry, and determination of strontium isotopes (87Sr/86Sr) in otoliths by laser ablation-ICPMS differentiated between freshwater and saltwater residence. Results showed that fish moving into freshwater floodplain wetlands concentrated mercury in muscle tissue at approximately twice the level of those that remained in saline habitats. Resolving life histories through otolith analyses demonstrated diversity in mercury bioaccumulation for individual fish of the same migratory contingent on the floodplains. Although trophic level (δ15N), capture location, source of nutrition (δ13C), and age or size partly predicted mercury concentrations in barramundi, our results suggest that individual variability in diets, migration patterns and potentially metabolism are also influential. Using a migratory fish as a bio-indicator, and tracking its life history and use of resources, proved valuable as a tool to discern hot spots in a coastal waterway for a contaminant, such as mercury.

Long-term dynamics and drivers of coral and macroalgal cover on inshore reefs of the Great Barrier Reef Marine Park.

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.

Development of the coral index, a summary of coral reef resilience as a guide for management.

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.

Delayed coral recovery in a warming ocean.

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.

Larval precompetency and settlement behaviour in 25 Indo-Pacific coral species.

Knowledge of coral larval precompetency periods and maximum competency windows is fundamental to understanding coral population dynamics, informing biogeography and connectivity patterns, and predicting reef recovery following disturbances. Yet for many species, estimates of these early-life history metrics are scarce and vary widely. Furthermore, settlement cues for many taxa are not known despite consequences to habitat selection. Here we performed a comprehensive experimental time-series investigation of larval settlement behaviour, for 25 Indo-Pacific broadcast-spawning species. To investigate the duration of precompetency, improve predictions of the competency windows, and compare settlement responses within and amongst species, we completed replicated and repeated 24-hour assays that exposed larvae to five common settlement cues. Our study revealed that larval competency in some broadcast-spawning species begins as early as two days post fertilization, but that the precompetency period varies within and between species from about two to six days, with consequences for local retention and population connectivity. We also found that larvae of some species are competent to settle beyond 70 days old and display complex temporal settlement behaviour, challenging the assumption that competency gradually wanes over time and adding to the evidence that larval longevity can support genetic connectivity and long-distance dispersal. Using these data, we grouped coral taxa by short, mid and long precompetency periods, and identified their preferred settlement cues. Taken together, these results inform our understanding of larval dynamics across a broad range of coral species and can be applied to investigations of population dynamics, connectivity, and reef recovery.

Physical, biological and anthropogenic drivers of spatial patterns of coral reef fish assemblages at regional and local scales.

Species abundance, diversity and community assemblage structure are determined by multiple physical, habitat and management drivers that operate across multiple spatial scales. Here we used a multi-scale coral reef monitoring dataset to examine regional and local differences in the abundance, species richness and composition of fish assemblages in no-take marine reserve (NTMR) and fished zones at four island groups in the Great Barrier Reef Marine Park, Australia. We applied boosted regression trees to quantify the influence of 20 potential drivers on the coral reef fish assemblages. Reefs in two locations, Magnetic Island and the Keppel Islands, had distinctive fish assemblages and low species richness, while the Palm and Whitsunday Islands had similar species composition and higher species richness. Overall, our analyses identified several important physical (temperature, wave exposure) and biological (coral, turf, macroalgal and unconsolidated substratum cover) drivers of inshore reef fish communities, some of which are being altered by human activities. Of these, sea surface temperature (SST) was more influential at large scales, while wave exposure was important both within and between island groups. Species richness declined with increasing macroalgal cover and exposure to cyclones, and increased with SST. Species composition was most strongly influenced by mean SST and percent cover of macroalgae. There was substantial regional variation in the local drivers of spatial patterns. Although NTMR zoning influenced total fish density in some regions, it had negligible effects on fish species richness, composition and trophic structure because of the relatively small number of species targeted by the fishery. These findings show that inshore reef fishes are directly influenced by disturbances typical of the nearshore Great Barrier Reef, highlighting the need to complement global action on climate change with more targeted localised efforts to maintain or improve the condition of coral reef habitats.

Developing an effective marine eDNA monitoring: eDNA detection at pre-outbreak densities of corallivorous seastar (Acanthaster cf. solaris).

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 was >0.8. 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-1). Copy number-based estimates may be more relevant to quantify CoTS at higher densities. Although water residence age did contribute little to our models, sites with higher residence times may serve as sentinel sites accumulating eDNA. The approach based on presence or absence of eDNA facilitates eDNA monitoring to detect CoTS densities below outbreak thresholds and we continue to further develop this method for quantification.

A benthic light index of water quality in the Great Barrier Reef, Australia.

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.

High spatio-temporal variability in Acroporidae settlement to inshore reefs of the Great Barrier Reef.

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.

Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment.

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.

Recovery from bleaching is mediated by threshold densities of background thermo-tolerant symbiont types in a reef-building coral.

Sensitive molecular analyses show that most corals host a complement of Symbiodinium genotypes that includes thermo-tolerant types in low abundance. While tolerant symbiont types are hypothesized to facilitate tolerance to temperature and recovery from bleaching, empirical data on their distribution and relative abundance in corals under ambient and stress conditions are still rare. We quantified visual bleaching and mortality of coral hosts, along with relative abundance of C- and D-type Symbiodinium cells in 82 Acropora millepora colonies from three locations on the Great Barrier Reef transplanted to a central inshore site over a 13 month period. Our analyses reveal dynamic change in symbiont associations within colonies and among populations over time. Coral bleaching and declines in C- but not D-type symbionts were observed in transplanted corals. Survival and recovery of 25% of corals from one population was associated with either initial D-dominance or an increase in D-type symbionts that could be predicted by a minimum pre-stress D : C ratio of 0.003. One-third of corals from this population became D dominated at the bleached stage despite no initial detection of this symbiont type, but failed to recover and died in mid to late summer. These results provide a predictive threshold minimum density of background D-type symbionts in A. millepora, above which survival following extreme thermal stress is increased.

Spatial and Temporal Variation in the Effects of Climatic Variables on Dugong Calf Production.

Knowledge of the relationships between environmental forcing and demographic parameters is important for predicting responses from climatic changes and to manage populations effectively. We explore the relationships between the proportion of sea cows (Dugong dugon) classified as calves and four climatic drivers (rainfall anomaly, Southern Oscillation El Niño Index [SOI], NINO 3.4 sea surface temperature index, and number of tropical cyclones) at a range of spatially distinct locations in Queensland, Australia, a region with relatively high dugong density. Dugong and calf data were obtained from standardized aerial surveys conducted along the study region. A range of lagged versions of each of the focal climatic drivers (1 to 4 years) were included in a global model containing the proportion of calves in each population crossed with each of the lagged versions of the climatic drivers to explore relationships. The relative influence of each predictor was estimated via Gibbs variable selection. The relationships between the proportion of dependent calves and the climatic drivers varied spatially and temporally, with climatic drivers influencing calf counts at sub-regional scales. Thus we recommend that the assessment of and management response to indirect climatic threats on dugongs should also occur at sub-regional scales.

Allelic variants of the Melanocortin 4 receptor (MC4R) gene in a South African study group.

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.

Zooplankton Growth, Respiration and Grazing on the Australian Margins of the Tropical Indian and Pacific Oceans.

The specific activity of aminoacyl-tRNA synthetases (spAARS), an index of growth rate, and of the electron transport system (spETS), an index of respiration, was measured in three size fractions (73-150 µm, >150 µm and >350 µm) of zooplankton during five cruises to tropical coastal waters of the Kimberley coast (North West Australia) and four cruises to waters of the Great Barrier Reef (GBR; North East Australia). The N-specific biomass of plankton was 3-4-fold higher in the Kimberley than on the GBR in all 3 size classes: Kimberley 1.27, 3.63, 1.94 mg m-3; GBR 0.36, 0.88 and 0.58 mg m-3 in the 73-150 µm, >150 µm and >350 µm size classes, respectively. Similarly, spAARS activity in the Kimberley was greater than that of the GBR: 88.4, 132.2, and 147.6 nmol PPi hr-1 mg protein -1 in the Kimberley compared with 71.7, 82.0 and 83.8 nmol PPi hr-1 mg protein -1 in the GBR, for the 73-150 µm, >150 µm and >350 µm size classes, respectively. Specific ETS activity showed similar differences in scale between the two coasts: 184.6, 148.8 and 92.2 µL O2 hr-1 mg protein-1 in the Kimberley, against 86.5, 88.3 and 71.3 µL O2 hr-1 mg protein-1 in the GBR. On the basis of these measurements, we calculated that >150 µm zooplankton grazing accounted for 7% of primary production in the Kimberley and 8% in GBR waters. Area-specific respiration by >73 µm zooplankton was 7-fold higher in the Kimberley than on the GBR and production by >150 µm zooplankton was of the order of 278 mg C m-2 d-1 in the Kimberley and 42 mg C m-2 d-1 on the GBR. We hypothesize that the much stronger physical forcing on the North West shelf is the principal driver of higher rates in the west than in the east of the continent.

Expectations and Outcomes of Reserve Network Performance following Re-zoning of the Great Barrier Reef Marine Park.

Networks of no-take marine reserves (NTMRs) are widely advocated for preserving exploited fish stocks and for conserving biodiversity. We used underwater visual surveys of coral reef fish and benthic communities to quantify the short- to medium-term (5 to 30 years) ecological effects of the establishment of NTMRs within the Great Barrier Reef Marine Park (GBRMP). The density, mean length, and biomass of principal fishery species, coral trout (Plectropomus spp., Variola spp.), were consistently greater in NTMRs than on fished reefs over both the short and medium term. However, there were no clear or consistent differences in the structure of fish or benthic assemblages, non-target fish density, fish species richness, or coral cover between NTMR and fished reefs. There was no indication that the displacement and concentration of fishing effort reduced coral trout populations on fished reefs. A severe tropical cyclone impacted many survey reefs during the study, causing similar declines in coral cover and fish density on both NTMR and fished reefs. However, coral trout biomass declined only on fished reefs after the cyclone. The GBRMP is performing as expected in terms of the protection of fished stocks and biodiversity for a developed country in which fishing is not excessive and targets a narrow range of species. NTMRs cannot protect coral reefs directly from acute regional-scale disturbance but, after a strong tropical cyclone, impacted NTMR reefs supported higher biomass of key fishery-targeted species and so should provide valuable sources of larvae to enhance population recovery and long-term persistence.

Phylogeny drives large scale patterns in Australian marine bioactivity and provides a new chemical ecology rationale for future biodiscovery.

Twenty-five years of Australian marine bioresources collecting and research by the Australian Institute of Marine Science (AIMS) has explored the breadth of latitudinally and longitudinally diverse marine habitats that comprise Australia's ocean territory. The resulting AIMS Bioresources Library and associated relational database integrate biodiversity with bioactivity data, and these resources were mined to retrospectively assess biogeographic, taxonomic and phylogenetic patterns in cytotoxic, antimicrobial, and central nervous system (CNS)-protective bioactivity. While the bioassays used were originally chosen to be indicative of pharmaceutically relevant bioactivity, the results have qualified ecological relevance regarding secondary metabolism. In general, metazoan phyla along the deuterostome phylogenetic pathway (eg to Chordata) and their ancestors (eg Porifera and Cnidaria) had higher percentages of bioactive samples in the assays examined. While taxonomy at the phylum level and higher-order phylogeny groupings helped account for observed trends, taxonomy to genus did not resolve the trends any further. In addition, the results did not identify any biogeographic bioactivity hotspots that correlated with biodiversity hotspots. We conclude with a hypothesis that high-level phylogeny, and therefore the metabolic machinery available to an organism, is a major determinant of bioactivity, while habitat diversity and ecological circumstance are possible drivers in the activation of this machinery and bioactive secondary metabolism. This study supports the strategy of targeting phyla from the deuterostome lineage (including ancestral phyla) from biodiverse marine habitats and ecological niches, in future biodiscovery, at least that which is focused on vertebrate (including human) health.

Ongoing effects of no-take marine reserves on commercially exploited coral trout populations on the Great Barrier Reef.

Networks of no-take marine reserves (NTMRs) are widely used for managing marine resources. Because they restrict fishing, managers need to monitor reserves to reassure stakeholders that they are achieving the intended results. In 2004, the Great Barrier Reef (GBR) Marine Park was rezoned and the area of NTMRs was greatly increased. Using manta tow we assessed the effectiveness of the new NTMRs in conserving coral trout (Plectropomus and Variola spp.), the principle targets of the GBR reef line fishery. Over a six year period, we sampled regional groups of matched pairs of similar reefs, ones closed to fishing under the rezoning and ones that remained open. Coral trout populations were significantly higher in NTMRs. While coral trout populations declined on reefs open to fishing, stocks were maintained in NTMRs, highlighting the ongoing benefits of marine reserves.