Quantifying parameter uncertainty in a coral reef model using Metropolis-Coupled Markov Chain Monte Carlo

Coral reefs are threatened ecosystems, so it is important to have predictive models of their dynamics. Most current models of coral reefs fall into two categories. The first is simple heuristic models which provide an abstract understanding of the possible behaviour of reefs in general, but do not describe real reefs. The second is complex simulations whose parameters are obtained from a range of sources such as literature estimates. We cannot estimate the parameters of these models from a single data set, and we have little idea of the uncertainty in their predictions.We have developed a compromise between these two extremes, which is complex enough to describe real reef data, but simple enough that we can estimate parameters for a specific reef from a time series. In previous work, we fitted this model to a long-term data set from Heron Island, Australia, using maximum likelihood methods. To evaluate predictions from this model, we need estimates of the uncertainty in our parameters. Here, we obtain such estimates using Bayesian Metropolis-Coupled Markov Chain Monte Carlo. We do this for versions of the model in which corals are aggregated into a single state variable (the three-state model), and in which corals are separated into four state variables (the six-state model), in order to determine the appropriate level of aggregation. We also estimate the posterior distribution of predicted trajectories in each case.In both cases, the fitted trajectories were close to the observed data, but we had doubts about the biological plausibility of some parameter estimates. We suggest that informative prior distributions incorporating expert knowledge may resolve this problem. In the six-state model, the posterior distribution of state frequencies after 40 years contained two divergent community types, one dominated by free space and soft corals, and one dominated by acroporid, pocilloporid, and massive corals. The three-state model predicts only a single community type. We conclude that the three-state model hides too much biological heterogeneity, but we need more data if we are to obtain reliable predictions from the six-state model. It is likely that there will be similarly large, but currently unevaluated, uncertainty in the predictions of other coral reef models, many of which are much more complex and harder to fit to real data.     

In situ exposures using caged organisms: a multi-compartment approach to detect aquatic toxicity and bioaccumulation

An in situ toxicity and bioaccumulation assessment approach is described to assess stressor exposure and effects in surface waters (low and high flow), the sediment-water interface, surficial sediments and pore waters (including groundwater upwellings). This approach can be used for exposing species, representing major functional and taxonomic groups. Pimephales promelas, Daphnia magna, Ceriodaphnia dubia, Hyalella azteca, Hyalella sp., Chironomus tentans, Lumbriculus variegatus, Hydra attenuatta, Hexagenia sp. and Baetis tibialis were successfully used to measure effects on survival, growth, feeding, and/or uptake. Stressors identified included chemical toxicants, suspended solids, photo-induced toxicity, indigenous predators, and flow. Responses varied between laboratory and in situ exposures in many cases and were attributed to differing exposure dynamics and sample-processing artifacts. These in situ exposure approaches provide unique assessment information that is complementary to traditional laboratory-based toxicity and bioaccumulation testing and reduce the uncertainties of extrapolating from the laboratory to field responses.     

Faunal relationships among the near-reef zooplankton at three locations on heron reef,great barrier reef,and seasonal changes in this fauna

Samples of zooplankton were collected using a light trap at 5 sites in 3 locations on Heron Reef: (a) near the surface of open water 300 m south of the reef crest; (b) near the surface and at the substratum on the upper reef slope; (c) near the surface and at the substratum on a patch reef in the Heron lagoon. The collections made were analysed with respect to: (a) distribution and abundance of the taxa present; (b) faunistic relationships among samples from the 5 sites; (c) seasonal changes in both of these factors. A total of 181 taxa were recognised, many of which are identified to species, and many of which are demersal or epi-benthic in habits. At all sites, the abundance of animals increases from May to November, and faunal similarity between sites also changes. In May, reef collections are generally similar to one another and, with the exception of the slope surface collection, distinct from the open water collection. In September this pattern is enhanced, but in November slope collections more closely resemble the open water collection, while the lagoon collections are quite distinct from slope and open water collections. Lagoon surface and substratum collections also differ considerably from each other at this time. A MULTCLAS cluster analysis of the samples confirms the pattern of change in faunal relationships seen from examination of the collections. Dark-trap samples were used to assess the bias introduced by using a light to attract the animals, as well as to estimate the density of the fauna sampled. Lighttrap samples over-represent calanoid and harpacticoid copepods and gammarid amphipods, but the bias is minor and does not prevent use of a light trap as an efficient sampling tool for near-reef plankton. The density of the fauna is approximately 700 animals m^-3 at all sites. This may be a lower density than in more tropical regions. Pronounced seasonal changes occur in faunal composition of collections from open water and from surface sites. The substratum collections show more constant faunas throughout the year. Major changes are primarily in the proportions of copepods and cumaceans present. Changes in amphipod numbers are also important at lagoon sites.     

Composition of the near-reef zooplankton at Heron Reef,Great Barrier Reef

Using a light trap, zooplankton was sampled at three stations at Heron Reef, Great Barrier Reef: (a) a typical patch reef in the Heron lagoon, (b) a site in 8 m water on the southern slope of Heron reef, and (c) a station approximately 300 m south of (b), in the open water of the channel between Heron and Wistari reefs. Samples were taken at the surface and on the substratum at the lagoon and reef-slope stations, and at 3 to 6 m depth at the open-water station. A total of 114 taxa, many recognized as species, were distinguished in the samples. Pronounced differences existed in abundance, diversity, and taxonomic composition of the samples obtained at different stations. Less pronounced differences existed between surface and substratum samples from the same station. Near-reef samples were more similar to one another than to open-water samples. Decapod larvae, amphipods, and cumaceans were all abundant in near-reef samples and very rare in open-water samples. Forams, isopods, mysids and polychaetes were common in near-reef samples, and rare or absent in open-water samples. Copepods were abundant in all samples but the near-reef samples contained predominantly different species than did samples from the open water. The near-reef fauna included 66 taxa which did not occur in open-water samples. Many of these were epibenthic rather than strictly planktonic in behaviour.