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Large tropical and sub-tropical marine animals must meet their energetic requirements in a largely oligotrophic environment. Many planktivorous elasmobranchs, whose thermal ecologies prevent foraging in nutrient-rich polar waters, aggregate seasonally at predictable locations throughout tropical oceans where they are observed feeding. Here we investigate the foraging and oceanographic environment around Lady Elliot Island, a known aggregation site for reef manta rays Manta alfredi in the southern Great Barrier Reef. The foraging behaviour of reef manta rays was analysed in relation to zooplankton populations and local oceanography, and compared to long-term sighting records of reef manta rays from the dive operator on the island. Reef manta rays fed at Lady Elliot Island when zooplankton biomass and abundance were significantly higher than other times. The critical prey density threshold that triggered feeding was 11.2 mg m-3 while zooplankton size had no significant effect on feeding. The community composition and size structure of the zooplankton was similar when reef manta rays were feeding or not, with only the density of zooplankton changing. Higher zooplankton biomass was observed prior to low tide, and long-term (~5 years) sighting data confirmed that more reef manta rays are also observed feeding during this tidal phase than other times. This is the first study to examine prey availability at an aggregation site for reef manta rays and it indicates that they feed in locations and at times of higher zooplankton biomass.

Assessing the trophic role and interaction of an animal is key to understanding its general ecology and dynamics. Conventional techniques used to elucidate diet, such as stomach content analysis, are not suitable for large threatened marine species. Non-lethal sampling combined with biochemical methods provides a practical alternative for investigating the feeding ecology of these species. Stable isotope and signature fatty acid analyses of muscle tissue were used for the first time to examine assimilated diet of the reef manta ray Manta alfredi, and were compared with different zooplankton functional groups (i.e. near-surface zooplankton collected during manta ray feeding events and non-feeding periods, epipelagic zooplankton, demersal zooplankton and several different zooplankton taxa). Stable isotope δ(15)N values confirmed that the reef manta ray is a secondary consumer. This species had relatively high levels of docosahexaenoic acid (DHA) indicating a flagellate-based food source in the diet, which likely reflects feeding on DHA-rich near-surface and epipelagic zooplankton. However, high levels of ω6 polyunsaturated fatty acids and slightly enriched δ(13)C values in reef manta ray tissue suggest that they do not feed solely on pelagic zooplankton, but rather obtain part of their diet from another origin. The closest match was with demersal zooplankton, suggesting it is an important component of the reef manta ray diet. The ability to feed on demersal zooplankton is likely linked to the horizontal and vertical movement patterns of this giant planktivore. These new insights into the habitat use and feeding ecology of the reef manta ray will assist in the effective evaluation of its conservation needs.

Manta rays Manta alfredi are present all year round at Lady Elliot Island (LEI) in the southern Great Barrier Reef, Australia, with peaks in abundance during autumn and winter. Drivers influencing these fluctuations in abundance of M. alfredi at the site remain uncertain. Based on daily count, behavioural, weather and oceanographic data collected over a three-year period, this study examined the link between the relative number of sightings of manta rays at LEI, the biophysical environment, and the habitat use of individuals around the LEI reef using generalised additive models. The response variable in each of the three generalised additive models was number of sightings (per trip at sea) of cruising, cleaning or foraging M. alfredi. We used a set of eleven temporal, meteorological, biological, oceanographic and lunar predictor variables. Results for cruising, cleaning and foraging M. alfredi explained 27.5%, 32.8% and 36.3% of the deviance observed in the respective models and highlighted five predictors (year, day of year, wind speed, chlorophyll-a concentration and fraction of moon illuminated) as common influences to the three models. There were more manta rays at LEI in autumn and winter, slower wind speeds, higher productivity, and around the new and full moon. The winter peak in sightings of foraging M. alfredi was found to precede peaks in cleaning and cruising activity around the LEI reef, which suggests that enhanced food availability may be a principal driver for this seasonal aggregation. A spatial analysis of behavioural observations highlighted several sites around the LEI reef as 'multi-purpose' areas where cleaning and foraging activities commonly occur, while the southern end of the reef is primarily a foraging area. The use of extensive citizen science datasets, such as those collected by dive operators in this study, is encouraged as they can provide valuable insights into a species' ecology.

The whale shark Rhincodon typus is an endangered, highly migratory species with a wide, albeit patchy, distribution through tropical oceans. Ten aerial survey flights along the southern Mozambican coast, conducted between 2004–2008, documented a relatively high density of whale sharks along a 200 km stretch of the Inhambane Province, with a pronounced hotspot adjacent to Praia do Tofo. To examine the residency and movement of whale sharks in coastal areas around Praia do Tofo, where they may be more susceptible to gill net entanglement, we tagged 15 juveniles with SPOT5 satellite tags and tracked them for 2–88 days (mean = 27 days) as they dispersed from this area. Sharks travelled between 10 and 2,737 km (mean = 738 km) at a mean horizontal speed of 28 ± 17.1 SD km day −1 . While several individuals left shelf waters and travelled across international boundaries, most sharks stayed in Mozambican coastal waters over the tracking period. We tested for whale shark habitat preferences, using sea surface temperature, chlorophyll- a concentration and water depth as variables, by computing 100 random model tracks for each real shark based on their empirical movement characteristics. Whale sharks spent significantly more time in cooler, shallower water with higher chlorophyll- a concentrations than model sharks, suggesting that feeding in productive coastal waters is an important driver of their movements. To investigate what this coastal habitat choice means for their conservation in Mozambique, we mapped gill nets during two dedicated aerial surveys along the Inhambane coast and counted gill nets in 1,323 boat-based surveys near Praia do Tofo. Our results show that, while whale sharks are capable of long-distance oceanic movements, they can spend a disproportionate amount of time in specific areas, such as along the southern Mozambique coast. The increasing use of drifting gill nets in this coastal hotspot for whale sharks is likely to be a threat to regional populations of this iconic species.

Manta rays are classified as Vulnerable to Extinction on the IUCN Red List for Threatened Species. In Australia, a key aggregation site for reef manta rays is Lady Elliot Island (LEI) on the Great Barrier Reef, ~7 km from the shelf edge. Here, we investigate the environmental processes that triggered the largest manta ray feeding aggregation yet observed in Australia, in early 2013. We use MODIS sea surface temperature (SST), chlorophyll-a concentration and photic depth data, together with in situ data, to show that anomalous river discharges led to high chlorophyll (anomalies: 10–15 mg∙m−3) and turbid (photic depth anomalies: −15 m) river plumes extending out to LEI, and that these became entrained offshore around the periphery of an active cyclonic eddy. Eddy dynamics led to cold bottom intrusions along the shelf edge (6 °C temperature decrease), and at LEI (5 °C temperature decrease). Strongest SST gradients (>1 °C∙km−1) were at the convergent frontal zone between the shelf and eddy-influenced waters, directly overlying LEI. Here, the front intensified on the spring ebb tide to attract and shape the aggregation pattern of foraging manta rays. Future research could focus on mapping the probability and persistence of these ecologically significant frontal zones via remote sensing to aid the management and conservation of marine species.

Whale sharks Rhincodon typus are globally threatened, but a lack of biological and demographic information hampers an accurate assessment of their vulnerability to further decline or capacity to recover. We used laser photogrammetry at two aggregation sites to obtain more accurate size estimates of free-swimming whale sharks compared to visual estimates, allowing improved estimates of biological parameters. Individual whale sharks ranged from 432-917 cm total length (TL) (mean ± SD = 673 ± 118.8 cm, N = 122) in southern Mozambique and from 420-990 cm TL (mean ± SD = 641 ± 133 cm, N = 46) in Tanzania. By combining measurements of stranded individuals with photogrammetry measurements of free-swimming sharks, we calculated length at 50% maturity for males in Mozambique at 916 cm TL. Repeat measurements of individual whale sharks measured over periods from 347-1,068 days yielded implausible growth rates, suggesting that the growth increment over this period was not large enough to be detected using laser photogrammetry, and that the method is best applied to estimating growth rates over longer (decadal) time periods. The sex ratio of both populations was biased towards males (74% in Mozambique, 89% in Tanzania), the majority of which were immature (98% in Mozambique, 94% in Tanzania). The population structure for these two aggregations was similar to most other documented whale shark aggregations around the world. Information on small (<400 cm) whale sharks, mature individuals, and females in this region is lacking, but necessary to inform conservation initiatives for this globally threatened species.

Most ocean color algorithms are designed for optically deep waters, where the seafloor has little or no effect on remote sensing reflectance. This can lead to inaccurate retrievals of inherent optical properties (IOPs) in optically shallow water environments. Here, we investigate in situ hyperspectral bottom reflectance signatures and their separability for coral reef waters, when observed at the spectral resolutions of MODIS and SeaWiFS sensors. We use radiative transfer modeling to calculate the effects of bottom reflectance on the remote sensing reflectance signal, and assess detectability and discrimination of common coral reef bottom classes by clustering modeled remote sensing reflectance signals. We assess 8280 scenarios, including four IOPs, 23 depths and 45 bottom classes at MODIS and SeaWiFS bands. Our results show: (i) no significant contamination (Rrscorr < 0.0005) of bottom reflectance on the spectrally-averaged remote sensing reflectance signal at depths >17 m for MODIS and >19 m for SeaWiFS for the brightest spectral reflectance substrate (light sand) in clear reef waters; and (ii) bottom cover classes can be combined into two distinct groups, “light” and “dark”, based on the modeled surface reflectance signals. This study establishes that it is possible to efficiently improve parameterization of bottom reflectance and water-column IOP retrievals in shallow water ocean color models for coral reef environments.

How do seabirds deal with intra-specific competition for food? We addressed this question in a study of the foraging behaviour of 91 Cape gannetsMorus capensisfrom 2 South African colonies, situated 110 km apart, using GPS and time-depth recorders. Theoretically birds should have widely overlapping foraging areas and comparable foraging characteristics. Surprisingly, the foraging areas only overlapped by 13 and 14%, and birds from the 2 colonies also showed marked differences in their foraging patterns. Birds from the larger colony foraged more intensively; their foraging trips lasted longer (22.6 vs 8.5 h), involving longer total flight time (7.8 vs 5.9 h), longer foraging path length (293 vs 228 km), and greater maximum distance from the breeding site (104 vs 67 km). They also travelled faster (50 vs 44 km h–1), and had a larger number of foraging locations during each trip (252 vs 121), with more sinuous foraging paths (1.4 vs 1.1). However, there were no significant differences in the number of dives per foraging trip (68 vs 66), the average maximum depth attained (3.4 vs 3.6 m), nor the average or total dive duration per foraging trip (4.3 vs 4.3 s and 5.7 vs 4.3 min, respectively). We conclude that gannets from these 2 colonies are spatially segregated and experience different foraging conditions. We speculate that wind patterns and group feeding could generate such foraging asymmetries. Foraging site fidelity and memory effects could consolidate these asymmetries, and generate ‘cultural’ differences in foraging patterns.

We investigate a range of indices to quantify upwelling on the central Great Barrier Reef (GBR), Australia, so that environmental and biological relationships associated with upwelling in this area can be explored. We show that \"Upwelling days\" (the number of days of upwelling) and diurnal variation in subsurface temperature (maximum-minimum, 20-m depth) are satisfactory metrics to describe the duration and intensity of upwelling events, respectively. We use these to examine key characteristics of shelf-break upwelling in the central GBR. Our results show, somewhat paradoxically, that although upwelling involves cold water being brought near to the surface, it is linked to positive thermal anomalies on the GBR, both locally and regionally. Summers (December to February) with strongest upwelling occurred during the GBR-wide bleaching events of 1997-1998 and 2001-2002. Upwelling in the GBR is enhanced during doldrums conditions that were a feature of these summers. During these conditions, the poleward-flowing East Australian Current flows faster, lifting the thermocline closer to the surface, spilling more sub-thermocline waters onto the shelf. Doldrums conditions also result in intense local heating, stratification of the water column, and, when severe, coral bleaching. Upwelling intrusions are spatially restricted (central GBR), generally remain subsurface, and are often intermittent, allowing GBR-wide bleaching to occur despite conditions resulting in enhanced upwelling. Intense upwelling events precede anomalous seasonal temperature maxima by up to 2 months and bleaching by 1-3 wk, leading to the prospect of using upwelling activity as a seasonal forecasting index of unusually warm summers and widespread bleaching.

Coral reefs are in decline worldwide and monitoring activities are important for assessing the impact of disturbance on reefs and tracking subsequent recovery or decline. Monitoring by field surveys provides accurate data but at highly localised scales and so is not cost-effective for reef scale monitoring at frequent time points. Remote sensing from satellites is an alternative and complementary approach. While remote sensing cannot provide the level of detail and accuracy at a single point than a field survey, the statistical power for inferring large scale patterns benefits in having complete areal coverage. This review considers the state of the art of coral reef remote sensing for the diverse range of objectives relevant for management, ranging from the composition of the reef: physical extent, benthic cover, bathymetry, rugosity; to environmental parameters: sea surface temperature, exposure, light, carbonate chemistry. In addition to updating previous reviews, here we also consider the capability to go beyond basic maps of habitats or environmental variables, to discuss concepts highly relevant to stakeholders, policy makers and public communication: such as biodiversity, environmental threat and ecosystem services. A clear conclusion of the review is that advances in both sensor technology and processing algorithms continue to drive forward remote sensing capability for coral reef mapping, particularly with respect to spatial resolution of maps, and synthesis across multiple data products. Both trends can be expected to continue.