Reply to the discussion by Karen Johannesson on “Rare earth element geochemistry of scleractinian coral skeleton during meteoric diagenesis: a sequence through neomorphism of aragonite to calcite” by Webb et al., Sedimentology, 56, 1433-1463

Webb et al. (2009) described a late Pleistocenecoral sample wherein the diagenetic stabilization of original coral aragonite to meteoric calcite was halted more or less mid-way through the process, allowing direct comparison of pre-diagenetic and post-diagenetic microstructure and trace element distributions. Those authors found that the rare earth elements (REEs) were relatively stable during meteoric diagenesis, unlike divalent cations such as Sr,and it was thus concluded that original, in this case marine, REE distributions potentially could be preserved through the meteoric carbonate stabilization process that must have affected many, if not most, ancient limestones. Although this was not the case in the analysed sample, they noted that where such diagenesis took place in laterally transported groundwater, trace elements derived from that groundwater could be incorporated into diagenetic calcite, thus altering the initial REE distribution (Banner et al., 1988). Hence, the paper was concerned with the diagenetic behaviour of REEs in a groundwater-dominated karst system. The comment offered by Johannesson (2011) does not question those research results, but rather, seeks to clarify an interpretation made by Webb et al. (2009) of an earlier paper, Johannesson et al. (2006).

Fusion or non fusion of coral fragments in Acropora

Corals inhabit high energy environments where frequent disturbances result in physical damage to coralla, including fragmentation, as well as generating and mobilizing large sediment clasts. The branching growth form common in the Acropora genus makes it particularly susceptible to such disturbances and therefore useful for study of the fate of large sediment clasts. Living Acropora samples with natural, extraneous, broken coral branches incorporated on their living surface and dead Acropora skeletons containing embedded clasts of isolated branch sections of Acropora were observed and/or collected from the reef flat of Heron Reef, southern Great Barrier Reef and Bargara, Australia respectively. Here we report three different outcomes when pebble-sized coral branches became lodged on living coral colonies during sedimentation events in natural settings in Acropora: 1) Where live coral branches produced during a disturbance event come to rest on probable genetic clone-mate colonies they become rapidly stabilised leading to complete soft tissue and skeletal fusion; 2) Where the branch and underlying colony are not clone-mates, but may still be the same or similar species, the branches still may be stabilised rapidly by soft tissue, but then one species will overgrow the other; and 3) Where branches represent dead skeletal debris, they are treated like any foreign clast and are surrounded by clypeotheca and incorporated into the corallum by overgrowth. The retention of branch fragments on colonies in high energy reef flat settings may suggest an active role of coral polyps to recognise and fuse with each other. Also, in all cases the healing of disturbed tissue and subsequent skeletal growth is an adaptation important for protecting colonies from invasion by parasites and other benthos following disturbance events and may also serve to increase corallum strength. Knowledge of such adaptations is important in studies of coral behaviour during periods of environmental stress.

Past 140-year environmental record in the northern South China Sea : evidence from coral skeletal trace metal variations

About 140-year changes in the trace metals in Porites coral samples from two locations in the northern South China Sea were investigated. Results of PCA analyses suggest that near the coast, terrestrial input impacted behavior of trace metals by 28.4%, impact of Sea Surface Temperature (SST) was 19.0%, contribution of war and infrastructure were 14.4% and 15.6% respectively. But for a location in the open sea, contribution of War and SST reached 33.2% and 16.5%, while activities of infrastructure and guano exploration reached 13.2% and 14.7%. While the spatiotemporal change model of Cu, Cd and Pb in seawater of the north area of South China Sea during 1986–1997 were reconstructed. It was found that in the sea area Cu and Cd contaminations were distributed near the coast while areas around Sanya, Hainan had high Pb levels because of the well-developed tourism related activities.

Mid-Holocene sea-level and coral reef demise : U-Th dating of subfossil corals in Moreton Bay, Australia

It is increasingly apparent that sea-level data (e.g. microfossil transfer functions, dated coral microatolls and direct observations from satellite and tidal gauges) vary temporally and spatially at regional to local scales, thus limiting our ability to model future sea-level rise for many regions. Understanding sealevel response at ‘far-field’ locations at regional scales is fundamental for formulating more relevant sea-level rise susceptibility models within these regions under future global change projections. Fossil corals and reefs in particular are valuable tools for reconstructing past sea levels and possible environmental phase shifts beyond the temporal constraints of instrumental records. This study used abundant surface geochronological data based on in situ subfossil corals and precise elevation surveys to determine previous sea level in Moreton Bay, eastern Australia, a far-field site. A total of 64 U-Th dates show that relative sea level was at least 1.1 m above modern lowest astronomical tide (LAT) from at least ˜6600 cal. yr BP. Furthermore, a rapid synchronous demise in coral reef growth occurred in Moreton Bay ˜5800 cal. yr BP, coinciding with reported reef hiatus periods in other areas around the Indo-Pacific region. Evaluating past reef growth patterns and phases allows for a better interpretation of anthropogenic forcing versus natural environmental/climatic cycles that effect reef formation and demise at all scales and may allow better prediction of reef response to future global change.

The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems

1.Marine ecosystems provide critically important goods and services to society, and hence their accelerated degradation underpins an urgent need to take rapid, ambitious and informed decisions regarding their conservation and management. 2.The capacity, however, to generate the detailed field data required to inform conservation planning at appropriate scales is limited by time and resource consuming methods for collecting and analysing field data at the large scales required. 3.The ‘Catlin Seaview Survey’, described here, introduces a novel framework for large-scale monitoring of coral reefs using high-definition underwater imagery collected using customized underwater vehicles in combination with computer vision and machine learning. This enables quantitative and geo-referenced outputs of coral reef features such as habitat types, benthic composition, and structural complexity (rugosity) to be generated across multiple kilometre-scale transects with a spatial resolution ranging from 2 to 6 m2. 4.The novel application of technology described here has enormous potential to contribute to our understanding of coral reefs and associated impacts by underpinning management decisions with kilometre-scale measurements of reef health. 5.Imagery datasets from an initial survey of 500 km of seascape are freely available through an online tool called the Catlin Global Reef Record. Outputs from the image analysis using the technologies described here will be updated on the online repository as work progresses on each dataset. 6.Case studies illustrate the utility of outputs as well as their potential to link to information from remote sensing. The potential implications of the innovative technologies on marine resource management and conservation are also discussed, along with the accuracy and efficiency of the methodologies deployed.

Geochemistry-based coral palaeoclimate studies and the potential of ‘non-traditional’ (non-massive Porites) corals : recent developments and future progression

Understanding the natural variability of the Earth's climate system and accurately identifying potential anthropogenic influences requires long term, geographically distributed records of key climate indicators, such as temperature and precipitation that extend prior to the last 400. years of the Holocene. Reef corals provide an excellent source of high resolution climate records, and importantly represent the tropical marine environment where palaeoclimate data are urgently required. Recent decades have seen significant improvement in our understanding of coral biomineralisation, the associated uptake of geochemical proxies and methods of identifying and understanding the effects of both early and late, post depositional diagenetic alteration. These processes all have significant implications for interpreting geochemical proxies relevant to palaeoclimatic reconstructions. This paper reviews the current 'state of the art' in terms of coral based palaeoclimate reconstructions and highlights a key remaining problem. The majority of coral based palaeoclimate research has been derived from massive colonies of Porites. However, massive Porites are not globally abundant and may not provide material of a particular age of interest in those regions where they are present. Therefore, there is great potential for alternate coral genera to act as complimentary climate archives. While it remains critical to consider five key factors - vital effects, differential growth morphologies, geochemical heterogeneity in the skeletal ultrastructure, transfer equation selection and diagenetic screening of skeletal material - in order to allow the highest level of accuracy in coral palaeoclimate reconstructions, it is also important to develop alternate taxa for palaeoclimate studies in regions where Porites colonies are absent or rare. Currently as many as nine genera other than Porites have proven at least limited utility in palaeothermometry, most of which are found in the Atlantic/Caribbean region where massive Porites do not exist. Even branching taxa such as Acropora have significant potential to preserve environmental archives. Increasing this capability will greatly expand the number of potential geochemical archives available for longer term temporal records of palaeoclimate.

Understanding Uncertainties in Non-Linear Population Trajectories: A Bayesian Semi-Parametric Hierarchical Approach to Large-Scale Surveys of Coral Cover

Recently, attempts to improve decision making in species management have focussed on uncertainties associated with modelling temporal fluctuations in populations. Reducing model uncertainty is challenging; while larger samples improve estimation of species trajectories and reduce statistical errors, they typically amplify variability in observed trajectories. In particular, traditional modelling approaches aimed at estimating population trajectories usually do not account well for nonlinearities and uncertainties associated with multi-scale observations characteristic of large spatio-temporal surveys. We present a Bayesian semi-parametric hierarchical model for simultaneously quantifying uncertainties associated with model structure and parameters, and scale-specific variability over time. We estimate uncertainty across a four-tiered spatial hierarchy of coral cover from the Great Barrier Reef. Coral variability is well described; however, our results show that, in the absence of additional model specifications, conclusions regarding coral trajectories become highly uncertain when considering multiple reefs, suggesting that management should focus more at the scale of individual reefs. The approach presented facilitates the description and estimation of population trajectories and associated uncertainties when variability cannot be attributed to specific causes and origins. We argue that our model can unlock value contained in large-scale datasets, provide guidance for understanding sources of uncertainty, and support better informed decision making

Non-market use and non-use values for preserving ecosystem services over time : a choice experiment application to coral reef ecosystems in New Caledonia

Non-use values (i.e. economic values assigned by individuals to ecosystem goods and services unrelated to current or future uses) provide one of the most compelling incentives for the preservation of ecosystems and biodiversity. Assessing the non-use values of non-users is relatively straightforward using stated preference methods, but the standard approaches for estimating non-use values of users (stated decomposition) have substantial shortcomings which undermine the robustness of their results. In this paper, we propose a pragmatic interpretation of non-use values to derive estimates that capture their main dimensions, based on the identification of a willingness to pay for ecosystem protection beyond one's expected life. We empirically test our approach using a choice experiment conducted on coral reef ecosystem protection in two coastal areas in New Caledonia with different institutional, cultural, environmental and socio-economic contexts. We compute individual willingness to pay estimates, and derive individual non-use value estimates using our interpretation. We find that, a minima, estimates of non-use values may comprise between 25 and 40% of the mean willingness to pay for ecosystem preservation, less than has been found in most studies.

Coastal development, coral reefs and marine life in Asia: Tourism's double-edged sword

A large proportion of the world's population, including those of Asian countries, live in close proximity to the coastline. Coastlines are being developed at a £aster rate than ever before and there is now a growing body of literature to show that such activities are affecting the quality of coastal ecosystems and its wildlife (see, for example, Jennings, 2004; Siler et al., 2014; Duke eta!., 2007). This in turn is impacting negatively on the fishing and the tourism industries, amongst others. Millions of people depend on these sectors for their livelihoods and, unsustainable development can only make the plight of those who rely on these resources worse. The tourism industry in the coastal regions is particularly at risk since the industry relies heavily on coastal ecosystems to attract visitors. This chapter discusses the strong links that exist between coastal development, tourism, marine ecosystems and its wildlife, drawing attention to two well-known species widely used in tourism, namely whales and sea turtles, and discussing their conservation in relation to tourism. The chapter is divided into six sections. The second section examines why it is important to strike a balance between coastal development and protecting ecosystems. In this section, we discuss the ma.ior identified causes of coastal ecosystem degradation from the published literature, and the third section focuses attention on tourism development in the Asian region, which is one of the major reasons for coastal degradation. A diagrammatic approach is used to illustrate that planning of coastal tourism development which takes into account environmental impacts could result in economic benefits to the areas and regions concerned. The negative impacts on tourism when coastal ecosystems are damaged are discussed in section four. Section five shows the economic benefits resulting from sea turtle and whale watching-based tourism in Australia, and section six examines tourism as a conservation tool. In this section, the differing experiences of sea turtle tourism in Sri Lanka and Australia are discussed based on our published work. The final section concludes.

Quantifying the state of populations and effects of disturbances at large spatio-temporal scales: The case of coral populations in the great barrier reef

This project was a step forward in applying statistical methods and models to provide new insights for more informed decision-making at large spatial scales. The model has been designed to address complicated effects of ecological processes that govern the state of populations and uncertainties inherent in large spatio-temporal datasets. Specifically, the thesis contributes to better understanding and management of the Great Barrier Reef.

Investigation of movement and factors influencing post-release survival of line-caught coral reef fish using recreational tag-recapture data

Six species of line-caught coral reef fish (Plectropomus spp., Lethrinus miniatus, Lethrinus laticaudis, Lutjanus sebae, Lutjanus malabaricus and Lutjanus erythropterus) were tagged by members of the Australian National Sportsfishing Association (ANSA) in Queensland between 1986 and 2003. Of the 14,757 fish tagged, 1607 were recaptured and we analysed these data to describe movement and determine factors likely to impact release survival. All species were classified as residents since over 80% of recaptures for each species occurred within 1 km of the release site. Few individuals (range 0.8-5%) were recaptured more than 20 km from their release point. L. sebae had a higher recapture rate (19.9%) than the other species studied (range 2.1-11.7%). Venting swimbladder gases, regardless of whether or not fish appeared to be suffering from barotrauma, significantly enhanced (P < 0.05) the survival of L. sebae and L. malabaricus but had no significant effect (P > 0.05) on L. erythropterus. The condition of fish on release, subjectively assessed by anglers, was only a significant effect on recapture rate for L. sebae where fish in "fair" condition had less than half the recapture rate of those assessed as in "excellent" or "good" condition. The recapture rate of L. sebae and L. laticaudis was significantly (P < 0.05) affected by depth with recapture rate declining in depths exceeding 30 m. Overall, the results showed that depth of capture, release condition and treatment for barotrauma influenced recapture rate for some species but these effects were not consistent across all species studied. Recommendations were made to the ANSA tagging clubs to record additional information such as injury, hooking location and hook type to enable a more comprehensive future assessment of the factors influencing release survival.

Effect of DNA extraction on ageing success in coral trout (Plectropomus leopardus) otoliths

To maximize the information commonly collected from otoliths, the effect of DNA extraction on the estimation of age with otoliths was evaluated by comparing sagittal otolith samples from common coral trout (Plectropomus leopardus) for clarity and ageing discrepancies in DNA-extracted and untreated control otoliths. The DNA extraction process had no significant effect, indicating that archived otoliths can be used as a source of DNA while retaining their utility for age estimation.

Phototropic growth in a reef flat acroporid branching coral species

Many terrestrial plants form complex morphological structures and will alter these growth patterns in response to light direction. Similarly reef building corals have high morphological variation across coral families, with many species also displaying phenotypic plasticity across environmental gradients. In particular, the colony geometry in branching corals is altered by the frequency, location and direction of branch initiation and growth. This study demonstrates that for the branching species Acropora pulchra, light plays a key role in axial polyp differentiation and therefore axial corallite development - the basis for new branch formation. A. pulchra branches exhibited a directional growth response, with axial corallites only developing when light was available, and towards the incident light. Field experimentation revealed that there was a light intensity threshold of 45 mu mol m(-2) s(-1), below which axial corallites would not develop and this response was blue light (408-508 nm) dependent. There was a twofold increase in axial corallite growth above this light intensity threshold and a fourfold increase in axial corallite growth under the blue light treatment. These features of coral branch growth are highly reminiscent of the initiation of phototropic branch growth in terrestrial plants, which is directed by the blue light component of sunlight.

Effects of climate change on reproduction,larval development, and adult health of coral trout (Plectropomus spp.)

Climate change is emerging as the single greatest threat to coral-reef ecosystems.The most immediate impacts will be a loss of diversity and changes to fish community composition and may lead to eventual declines in abundance and productivity of key fisheries species. A key component of this research is to assess effects of projected changes in environmental conditions (temperature and ocean acidity) due to climate change on reproduction, growth and development of coral trout (Plectropomus leopardis).Ultimately, this research will fill key knowledge gaps about climate change impacts on larger fishes, which are fundamental to optimizing resilience-based management, and in turn improve the adaptive capacity of industries and communities along the Great Barrier Reef.