Relative influence of environmental factors on the timing and occurrence of multi-species coral reef fish aggregations

Reef configuration and hydrodynamics were identified as the principle physical drivers behind coral reef fish aggregations on a mid-shelf patch reef in the northern section of the Great Barrier Reef (-16.845°, 146.23°). The study was carried out over a six-year period at a large reef pass on the oceanic margin of the northern Great Barrier Reef. Over this period (February 2006 –December 2012) tidal state, moon phase and surface seawater temperature were monitored. The timing of sampling was organised to assess variation in physical environment at daily, monthly, seasonal and annual time scales. Over these time scales, temporal patterns of occurrence of 10 species of coral reef fish from 5 families representing 5 defined trophic groups were monitored. The study incorporated 1,357 underwater visual census counts involving 402,370 fish and these estimates were collated with data on tidal state, water temperature, lunar and seasonal periodicity. Aggregated boosted regression trees analysed the univariate responses of fish abundance and species richness to the variation in the physical environment of the reef pass. Flood tides or when water flows from open water through the pass and into the Moore Reef lagoon had 2.3 times as many fish and 1.75 times as many species compared to counts made on ebb tides. Fish abundance was highest in late winter and spring months (Austral calendar), but notably when water temperatures were below the long-term mean of 27°C. Multivariate regression trees and Dufrêne-Legendre indicator predicted 4 out of 10 times the occurrence of all 10 species at any temporal scale ranging from hours to years. Flood tides were the principle driver underlying the occurrence of all 10 species regardless of their trophic classification and produced distinct seasonal assemblages, indicative of fishes aggregating to forage and reproduce

James's rule and causes and consequences of a latitudinal cline in the demography of John's Snapper (Lutjanus johnii) in coastal waters of Australia

Demographic parameters were derived from sectioned otoliths of John’s Snapper (Lutjanus johnii) from 4 regions across 9° of latitude and 23° of longitude in northern Australia. Latitudinal variation in size and growth rates of this species greatly exceeded longitudinal variation. Populations of John’s Snapper farthest from the equator had the largest body sizes, in line with James’s rule, and the fastest growth rates, contrary to the temperature-size rule for ectotherms. A maximum age of 28.6 years, nearly 3 times previous estimates, was recorded and the largest individual was 990 mm in fork length. Females grew to a larger mean asymptotic fork length (L∞) than did males, a finding consistent with functional gonochorism. Otolith weight at age and gonad weight at length followed the same latitudinal trends seen in length at age. Length at maturity was ~72–87% of L∞ and varied by ~23% across the full latitudinal gradient, but age at first maturity was consistently in the range of 6–10 years, indicating that basic growth trajectories were similar across vastly different environments. We discuss both the need for complementary reproductive data in age-based studies and the insights gained from experiments where the concept of oxygen- and capacity-limited thermal tolerance is applied to explain the mechanistic causes of James’s rule in tropical fish species

Deep-reef fish communities of the Great Barrier Reef shelf-break: trophic structure and habitat associations

The ecology of habitats along the Great Barrier Reef (GBR) shelf-break has rarely been investigated. Thus, there is little understanding of how associated fishes interact with deeper environments. We examined relationships between deep-reef fish communities and benthic habitat structure. We sampled 48 sites over a large depth gradient (54–260 m) in the central GBR using Baited Remote Underwater Video Stations and multibeam sonar. Fish community composition differed both among multiple shelf-break reefs and habitats within reefs. Epibenthic cover decreased with depth. Deep epibenthic cover included sponges, corals, and macro-algae, with macro-algae present to 194 m. Structural complexity decreased with depth, with more calcified reef, boulders, and bedrock in shallower depths. Deeper sites were flatter and more homogeneous with softer substratum. Habitats were variable within depth strata and were reflected in different fish assemblages among sites and among locations. Overall, fish trophic groups changed with depth and included generalist and benthic carnivores, piscivores, and planktivores while herbivores were rare below 50 m. While depth influenced where trophic groups occurred, site orientation and habitat morphology determined the composition of trophic groups within depths. Future conservation strategies will need to consider the vulnerability of taxa with narrow distributions and habitat requirements in unique shelf-break environments

A field and video-annotation guide for baited remote underwater stereo-video surveys of demersal fish assemblages

Researchers TL, BG, JW, NB and JM were supported by the Marine Biodiversity Hub through funding from the Australian Government's National Environmental Science Program. Data validation scripts and GlobalArchive.org were supported by the Australian Research Data Commons, the Gorgon-Barrow Island Gorgon Barrow Island Net Conservation Benefits Fund, administered by the Government of Western Australia and the BHP/UWA Biodiversity and Societal Benefits of Restricted Access Areas collaboration.1. Baited remote underwater stereo-video systems (stereo-BRUVs) are a popular tool to sample demersal fish assemblages and gather data on their relative abundance and body-size structure in a robust, cost-effective, and non-invasive manner. Given the rapid uptake of the method, subtle differences have emerged in the way stereo-BRUVs are deployed and how the resulting imagery are annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broad-scale insights into the dynamics of ecological systems. 2. We provide the first globally accepted guide for using stereo-BRUVs to survey demersal fish assemblages and associated benthic habitats. 3. Information on stereo-BRUV design, camera settings, field operations, and image annotation are outlined. Additionally, we provide links to protocols for data validation, archiving, and sharing. 4. Globally, the use of stereo-BRUVs is spreading rapidly. We provide a standardised protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable, and Reproducible (FAIR) workflows to increase the ability to synthesise global datasets and answer a broad suite of ecological questions.Publisher PDFPeer reviewe

Movements of Diadromous Fish in Large Unregulated Tropical Rivers Inferred from Geochemical Tracers

Patterns of migration and habitat use in diadromous fishes can be highly variable among individuals. Most investigations into diadromous movement patterns have been restricted to populations in regulated rivers, and little information exists for those in unregulated catchments. We quantified movements of migratory barramundi Lates calcarifer (Bloch) in two large unregulated rivers in northern Australia using both elemental (Sr/Ba) and isotope (87Sr/86Sr) ratios in aragonitic ear stones, or otoliths. Chemical life history profiles indicated significant individual variation in habitat use, particularly among chemically distinct freshwater habitats within a catchment. A global zoning algorithm was used to quantify distinct changes in chemical signatures across profiles. This algorithm identified between 2 and 6 distinct chemical habitats in individual profiles, indicating variable movement among habitats. Profiles of 87Sr/86Sr ratios were notably distinct among individuals, with highly radiogenic values recorded in some otoliths. This variation suggested that fish made full use of habitats across the entire catchment basin. Our results show that unrestricted movement among freshwater habitats is an important component of diadromous life histories for populations in unregulated systems

Development of a baited video technique and spatial models to explain patterns of fish biodiversity in inter-reef waters

A baited, remote, underwater video sampling technique (BRUVS) was developed to survey the patterns of diversity and abundance of fishes, sharks, rays and sea snakes in all shelf depths and ‘inter-reef’ habitats throughout the Great Barrier Reef Marine Park (GBRMP). The use of bait greatly enhanced the ability to distinguish fish assemblages, including those containing functional groups thought to be either unresponsive to bait, or shy of the carnivores present in the field of view (e.g. scarids and siganids). A field comparison showed the BRUVS recorded more, larger, mobile species (e.g. carangids, scombrids, carcharhinids) than demersal trawls and performed best in daylight hours. Although the BRUVS did not record many sedentary and cryptic families collected as trawl ‘bycatch fauna’ (e.g. apogonids, priacanthids, pleuronectiformes), they did discriminate the same site groups – and with less classification error than the trawls. BRUVS could be used on any seafloor topography and any zone of the GBRMP, but their effectiveness was restricted by high turbidity and low irradiance at the seabed. As a result, BRUVS sampling was included in the largest exploration yet undertaken of seafloor biodiversity on a tropical shelf. Replicate BRUVS were deployed at 366 sites throughout the length (‘along’) and breadth (‘across’) of the GBRMP, enabling a comprehensive examination of the spatial patterns in vertebrate richness, assemblage structure and species occurrences in terms of the major environmental covariates presumed to govern fish distributions. These analyses were conducted with gradient boosting models and multivariate classification and regression trees. These approaches are robust and flexible and allow visualisation of complex interactions. The latitudinal gradient in richness of the 347 species was relatively weak, but there were strong cross-shelf gradients, with a ‘hump shaped’ peak in richness about a position ~0.8 ‘across’ the shelf. This was shown not to be the result of a random, mid-domain effect in species ranges but rather a response to the topographic complexity, epibenthic marine plants, low currents and mixed carbonate/mud sediments found (on average) at this position. Hierarchical, multivariate regression tree analyses (MRT) constrained by 28 selected environmental covariates, showed ten assemblages characterised by Dufrêne-Legendre species indicators. There were strong faunal boundaries, or ecotones, about Bowen in the south and Cooktown to Cape Flattery in the north. A position about ~0.5-0.8 across the continental shelf, where carbonate content of the sediments rose to ~84%, separated inshore ‘lagoonal’ assemblages from offshore ‘reefal’ assemblages. On either side of this demarcation there were fish assemblages distinguished by their association with finer or coarse\ud sediments, beds of seagrass (Halophila) and banks of marine algae (Halimeda and others). There were more lethrinids, labrids, serranids and scarids offshore, but there was not strong replacement or zonation of vertebrate families along environmental gradients – unlike the generalisations from low latitude shelves in the Atlantic. Instead, there were changes amongst species within genera that followed sedimentary facies and other gradients. In the central section such gradients varied simply with position across the shelf, for example, from Nemipterus hexodon and N. peronii inshore, to N. furcosus and N. nematopus on the mid-shelf, to N. balinensoides on the outer shelf. Ubiquitous families of the highly evolved tetraodontiformes had advanced dentition and anti-predator defenses that no doubt enabled them to take advantage of the abundant, but often poor quality, sources of food in the vast plains of muddy and carbonate sediments. Boosted regression trees (BRT) were used to predict species responses to the environmental covariates, to identify important gradients and understand surrogacy and competition amongst the spatial and environmental predictors in models. The position of sites across and along the shelf gave the most parsimonious and easily interpretable models of species richness and assemblage structure, but the underlying gradients in properties of the sediments, epibenthos and water column were not so linear in these two dimensions. There were clearly three sections of the GBRMP, separated by ecotones, which differed in their flushing regime, tidal energy, oceanic influences, epibenthic habitats and sedimentary facies. The species responses and assemblage structure are discussed in terms of these influences on benthic communities and productivity of the water column, the functional morphology of the inter-reef vertebrates and the prevailing paradigms for tropical shelf faunas. In this study I conclude that spatial position and depth on linear tropical shelves are fundamental surrogates to provide insight on the major environmental drivers acting together to shape spatial gradients in vertebrate distributions, as well as identifying boundaries for management interventions

Inter-reef vertebrate communities of the Great Barrier Reef Marine Park determined by baited remote underwater video stations.

A fleet of baited remote underwater video stations was set in lagoonal and inter-reef waters of the Great Barrier Reef Marine Park, across 14° of latitude and the entire shelf. Counts of the maximum number seen in any one field of view were used to estimate relative abundance of 347 species of bony fishes, cartilaginous fishes and sea snakes. Boosted regression trees were used to assess the influence of depth and location of sampling sites on species richness. Multivariate regression trees and indices of specificity and fidelity (Dufrêne-Legendre indices) were used to distinguish 17 spatially contiguous vertebrate groups within a hierarchy of spatial scales. Location across the shelf and depth had the greatest influence on species richness, with peaks occurring around the ~35 m isobath in the inter-reef waters of the reef matrix, coinciding with shallow banks and shoals. Richness increased slightly toward the equator. Nine terminal vertebrate communities parallel to the coast were distinguished inshore and offshore in deep and shallow water along a latitudinal gradient. There were important community boundaries at Bowen in the south, Townsville in the centre, and Cape Flattery in the north. Latitudinal groupings were most evident inshore. Offshore communities were spatially extensive and separated lagoonal, mid-shelf and outer-shelf sites. Community boundaries were correlated with knowledge of strong gradients in sedimentary and oceanographic processes influenced by the shape of the reef matrix and regional tides and currents

Deep-reef fish assemblages of the Great Barrier Reef shelf-break (Australia)

Abstract Tropical mesophotic and sub-mesophotic fish ecology is poorly understood despite increasing vulnerability of deeper fish assemblages. Worldwide there is greater fishing pressure on continental shelf-breaks and the effects of disturbances on deeper fish species have not yet been assessed. Difficult to access, deeper reefs host undocumented fish diversity and abundance. Baited Remote Underwater Video Stations (BRUVS) with lights were used to sample deeper habitats (54–260 m), in the Great Barrier Reef (GBR), Australia. Here we describe fish biodiversity, relative abundance and richness, assessing the prediction that depth would drive assemblage structure in the GBR. Distinct groups of fishes were found with depth whilst overall richness and abundance decreased steeply between 100 and 260 m. Commercially-valuable Lutjanidae species from Pristipomoides and Etelis genera, were absent from shallower depths. Few fish species overlapped between adjacent depth strata, indicating unique assemblages with depth. We also detected new location records and potential new species records. The high biodiversity of fish found in shelf-break environments is poorly appreciated and depth is a strong predictor of assemblage composition. This may pose a challenge for managers of commercial fisheries as distinct depth ranges of taxa may translate to more readily targeted habitats, and therefore, an inherent vulnerability to exploitation

Tracing the life history of individual Barramundi using laser ablation MC-ICP-MS Sr-isotopic and Sr/Ba ratios in otoliths

Otoliths preserve a continuous geochemical record of its life history, from the earliest natal stage through to adulthood. Using in situ laser ablation (UV) multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) measurements of Sr isotopic compositions together with elemental abundances (Ca, Sr, Ba and Mg), we show how it is possible to characterise the various types of habitats encountered throughout the lifecycle history of individual barramundi. Unlike trace element concentrations, which can be modulated by physiological processes, Sr isotopic compositions of otoliths provide a direct fingerprint of the water mass in which the fish lived. Elemental abundances, in particular Sr/Ba ratios are, however, shown to be especially sensitive to transitional environments, such as estuaries. The flexibility of the barramundi's life history is confirmed by the present study, with the existence of both marine and freshwater nurseries, with some individuals spending their entire life cycle in fresh water, some entirely in marine and others moving between freshwater estuarine and marine habitats