Discerning the timing and cause of historical mortality events in modern Porites from the Great Barrier Reef

The life history strategies of massive Porites corals make them a valuable resource not only as key providers of reef structure, but also as recorders of past environmental change. Yet recent documented evidence of an unprecedented increase in the frequency of mortality in Porites warrants investigation into the history of mortality and associated drivers. To achieve this, both an accurate chronology and an understanding of the life history strategies of Porites are necessary. Sixty-two individual Uranium–Thorium (U–Th) dates from 50 dead massive Porites colonies from the central inshore region of the Great Barrier Reef (GBR) revealed the timing of mortality to have occurred predominantly over two main periods from 1989.2 ± 4.1 to 2001.4 ± 4.1, and from 2006.4 ± 1.8 to 2008.4 ± 2.2 A.D., with a small number of colonies dating earlier. Overall, the peak ages of mortality are significantly correlated with maximum sea-surface temperature anomalies. Despite potential sampling bias, the frequency of mortality increased dramatically post-1980. These observations are similar to the results reported for the Southern South China Sea. High resolution measurements of Sr/Ca and Mg/Ca obtained from a well preserved sample that died in 1994.6 ± 2.3 revealed that the time of death occurred at the peak of sea surface temperatures (SST) during the austral summer. In contrast, Sr/Ca and Mg/Ca analysis in two colonies dated to 2006.9 ± 3.0 and 2008.3 ± 2.0, suggest that both died after the austral winter. An increase in Sr/Ca ratios and the presence of low Mg-calcite cements (as determined by SEM and elemental ratio analysis) in one of the colonies was attributed to stressful conditions that may have persisted for some time prior to mortality. For both colonies, however, the timing of mortality coincides with the 4th and 6th largest flood events reported for the Burdekin River in the past 60 years, implying that factors associated with terrestrial runoff may have been responsible for mortality. Our results show that a combination of U–Th and elemental ratio geochemistry can potentially be used to precisely and accurately determine the timing and season of mortality in modern massive Porites corals. For reefs where long-term monitoring data are absent, the ability to reconstruct historical events in coral communities may prove useful to reef managers by providing some baseline knowledge on disturbance history and associated drivers.

Load estimation with uncertainties from opportunistic sampling data: A semiparametric approach

We consider estimating the total load from frequent flow data but less frequent concentration data. There are numerous load estimation methods available, some of which are captured in various online tools. However, most estimators are subject to large biases statistically, and their associated uncertainties are often not reported. This makes interpretation difficult and the estimation of trends or determination of optimal sampling regimes impossible to assess. In this paper, we first propose two indices for measuring the extent of sampling bias, and then provide steps for obtaining reliable load estimates that minimizes the biases and makes use of informative predictive variables. The key step to this approach is in the development of an appropriate predictive model for concentration. This is achieved using a generalized rating-curve approach with additional predictors that capture unique features in the flow data, such as the concept of the first flush, the location of the event on the hydrograph (e.g. rise or fall) and the discounted flow. The latter may be thought of as a measure of constituent exhaustion occurring during flood events. Forming this additional information can significantly improve the predictability of concentration, and ultimately the precision with which the pollutant load is estimated. We also provide a measure of the standard error of the load estimate which incorporates model, spatial and/or temporal errors. This method also has the capacity to incorporate measurement error incurred through the sampling of flow. We illustrate this approach for two rivers delivering to the Great Barrier Reef, Queensland, Australia. One is a data set from the Burdekin River, and consists of the total suspended sediment (TSS) and nitrogen oxide (NO(x)) and gauged flow for 1997. The other dataset is from the Tully River, for the period of July 2000 to June 2008. For NO(x) Burdekin, the new estimates are very similar to the ratio estimates even when there is no relationship between the concentration and the flow. However, for the Tully dataset, by incorporating the additional predictive variables namely the discounted flow and flow phases (rising or recessing), we substantially improved the model fit, and thus the certainty with which the load is estimated.

Impact of climate variability on Plasmodium vivax and Plasmodium falciparum malaria in Yunnan Province, China

BACKGROUND Malaria remains a public health problem in the remote and poor area of Yunnan Province, China. Yunnan faces an increasing risk of imported malaria infections from Mekong river neighboring countries. This study aimed to identify the high risk area of malaria transmission in Yunnan Province, and to estimate the effects of climatic variability on the transmission of Plasmodium vivax and Plasmodium falciparum in the identified area. METHODS We identified spatial clusters of malaria cases using spatial cluster analysis at a county level in Yunnan Province, 2005-2010, and estimated the weekly effects of climatic factors on P. vivax and P. falciparum based on a dataset of daily malaria cases and climatic variables. A distributed lag nonlinear model was used to estimate the impact of temperature, relative humidity and rainfall up to 10-week lags on both types of malaria parasite after adjusting for seasonal and long-term effects. RESULTS The primary cluster area was identified along the China-Myanmar border in western Yunnan. A 1°C increase in minimum temperature was associated with a lag 4 to 9 weeks relative risk (RR), with the highest effect at lag 7 weeks for P. vivax (RR = 1.03; 95% CI, 1.01, 1.05) and 6 weeks for P. falciparum (RR = 1.07; 95% CI, 1.04, 1.11); a 10-mm increment in rainfall was associated with RRs of lags 2-4 weeks and 9-10 weeks, with the highest effect at 3 weeks for both P. vivax (RR = 1.03; 95% CI, 1.01, 1.04) and P. falciparum (RR = 1.04; 95% CI, 1.01, 1.06); and the RRs with a 10% rise in relative humidity were significant from lag 3 to 8 weeks with the highest RR of 1.24 (95% CI, 1.10, 1.41) for P. vivax at 5-week lag. CONCLUSIONS Our findings suggest that the China-Myanmar border is a high risk area for malaria transmission. Climatic factors appeared to be among major determinants of malaria transmission in this area. The estimated lag effects for the association between temperature and malaria are consistent with the life cycles of both mosquito vector and malaria parasite. These findings will be useful for malaria surveillance-response systems in the Mekong river region.

Linking ecological condition and the soundscape in fragmented Australian forests

Natural landscapes are increasingly subjected to anthropogenic pressure and fragmentation resulting in reduced ecological condition. In this study we examined the relationship between ecological condition and the soundscape in fragmented forest remnants of south-east Queensland, Australia. The region is noted for its high biodiversity value and increased pressure associated with habitat fragmentation and urbanisation. Ten sites defined by a distinct open eucalypt forest community dominated by spotted gum (Corymbia citriodora ssp. variegata) were stratified based on patch size and patch connectivity. Each site underwent a series of detailed vegetation condition and landscape assessments, together with bird surveys and acoustic analysis using relative soundscape power. Univariate and multivariate analyses indicated that the measurement of relative soundscape power reflects ecological condition and bird species richness, and is dependent on the extent of landscape fragmentation. We conclude that acoustic monitoring technologies provide a cost effective tool for measuring ecological condition, especially in conjunction with established field observations and recordings.

An extended regression approach to estimating loads and their uncertainties in Great Barrier Reef catchments

There are numerous load estimation methods available, some of which are captured in various online tools. However, most estimators are subject to large biases statistically, and their associated uncertainties are often not reported. This makes interpretation difficult and the estimation of trends or determination of optimal sampling regimes impossible to assess. In this paper, we first propose two indices for measuring the extent of sampling bias, and then provide steps for obtaining reliable load estimates by minimizing the biases and making use of possible predictive variables. The load estimation procedure can be summarized by the following four steps: - (i) output the flow rates at regular time intervals (e.g. 10 minutes) using a time series model that captures all the peak flows; - (ii) output the predicted flow rates as in (i) at the concentration sampling times, if the corresponding flow rates are not collected; - (iii) establish a predictive model for the concentration data, which incorporates all possible predictor variables and output the predicted concentrations at the regular time intervals as in (i), and; - (iv) obtain the sum of all the products of the predicted flow and the predicted concentration over the regular time intervals to represent an estimate of the load. The key step to this approach is in the development of an appropriate predictive model for concentration. This is achieved using a generalized regression (rating-curve) approach with additional predictors that capture unique features in the flow data, namely the concept of the first flush, the location of the event on the hydrograph (e.g. rise or fall) and cumulative discounted flow. The latter may be thought of as a measure of constituent exhaustion occurring during flood events. The model also has the capacity to accommodate autocorrelation in model errors which are the result of intensive sampling during floods. Incorporating this additional information can significantly improve the predictability of concentration, and ultimately the precision with which the pollutant load is estimated. We also provide a measure of the standard error of the load estimate which incorporates model, spatial and/or temporal errors. This method also has the capacity to incorporate measurement error incurred through the sampling of flow. We illustrate this approach using the concentrations of total suspended sediment (TSS) and nitrogen oxide (NOx) and gauged flow data from the Burdekin River, a catchment delivering to the Great Barrier Reef. The sampling biases for NOx concentrations range from 2 to 10 times indicating severe biases. As we expect, the traditional average and extrapolation methods produce much higher estimates than those when bias in sampling is taken into account.

Weather variability, tides, and Barmah Forest Virus Disease in the Gladstone region, Australia

In this study we examined the impact of weather variability and tides on the transmission of Barmah Forest virus (BFV) disease and developed a weather-based forecasting model for BFV disease in the Gladstone region, Australia. We used seasonal autoregressive integrated moving-average (SARIMA) models to determine the contribution of weather variables to BFV transmission after the time-series data of response and explanatory variables were made stationary through seasonal differencing. We obtained data on the monthly counts of BFV cases, weather variables (e.g., mean minimum and maximum temperature, total rainfall, and mean relative humidity), high and low tides, and the population size in the Gladstone region between January 1992 and December 2001 from the Queensland Department of Health, Australian Bureau of Meteorology, Queensland Department of Transport, and Australian Bureau of Statistics, respectively. The SARIMA model shows that the 5-month moving average of minimum temperature (β = 0.15, p-value < 0.001) was statistically significantly and positively associated with BFV disease, whereas high tide in the current month (β = −1.03, p-value = 0.04) was statistically significantly and inversely associated with it. However, no significant association was found for other variables. These results may be applied to forecast the occurrence of BFV disease and to use public health resources in BFV control and prevention.

Geographic Variation of Notified Ross River Virus Infections in Queensland, Australia, 1985-1996

The spatial and temporal variations of Ross River virus infections reported in Queensland, Australia, between 1985 and 1996 were studied by using the Geographic Information System. The notified cases of Ross River virus infection came from 489 localities between 1985 and 1988, 805 between 1989 and 1992, and 1,157 between 1993 and 1996 (chi2(df = 2) = 680.9; P < 0.001). There was a marked increase in the number of localities where the cases were reported by 65 percent for the period of 1989-1992 and 137 percent for 1993-1996, compared with that for 1985-1988. The geographic distribution of the notified Ross River virus cases has expanded in Queensland over recent years. As Ross River virus disease has impacted considerably on tourism and industry, as well as on residents of affected areas, more research is required to explore the causes of the geographic expansion of the notified Ross River virus infections.

Groundwater flow model of the Logan river alluvial aquifer system Josephville, South East Queensland

The study focuses on an alluvial plain situated within a large meander of the Logan River at Josephville near Beaudesert which supports a factory that processes gelatine. The plant draws water from on site bores, as well as the Logan River, for its production processes and produces approximately 1.5 ML per day (Douglas Partners, 2004) of waste water containing high levels of dissolved ions. At present a series of treatment ponds are used to aerate the waste water reducing the level of organic matter; the water is then used to irrigate grazing land around the site. Within the study the hydrogeology is investigated, a conceptual groundwater model is produced and a numerical groundwater flow model is developed from this. On the site are several bores that access groundwater, plus a network of monitoring bores. Assessment of drilling logs shows the area is formed from a mixture of poorly sorted Quaternary alluvial sediments with a laterally continuous aquifer comprised of coarse sands and fine gravels that is in contact with the river. This aquifer occurs at a depth of between 11 and 15 metres and is overlain by a heterogeneous mixture of silts, sands and clays. The study investigates the degree of interaction between the river and the groundwater within the fluvially derived sediments for reasons of both environmental monitoring and sustainability of the potential local groundwater resource. A conceptual hydrogeological model of the site proposes two hydrostratigraphic units, a basal aquifer of coarse-grained materials overlain by a thick semi-confining unit of finer materials. From this, a two-layer groundwater flow model and hydraulic conductivity distribution was developed based on bore monitoring and rainfall data using MODFLOW (McDonald and Harbaugh, 1988) and PEST (Doherty, 2004) based on GMS 6.5 software (EMSI, 2008). A second model was also considered with the alluvium represented as a single hydrogeological unit. Both models were calibrated to steady state conditions and sensitivity analyses of the parameters has demonstrated that both models are very stable for changes in the range of ± 10% for all parameters and still reasonably stable for changes up to ± 20% with RMS errors in the model always less that 10%. The preferred two-layer model was found to give the more realistic representation of the site, where water level variations and the numerical modeling showed that the basal layer of coarse sands and fine gravels is hydraulically connected to the river and the upper layer comprising a poorly sorted mixture of silt-rich clays and sands of very low permeability limits infiltration from the surface to the lower layer. The paucity of historical data has limited the numerical modelling to a steady state one based on groundwater levels during a drought period and forecasts for varying hydrological conditions (e.g. short term as well as prolonged dry and wet conditions) cannot reasonably be made from such a model. If future modelling is to be undertaken it is necessary to establish a regular program of groundwater monitoring and maintain a long term database of water levels to enable a transient model to be developed at a later stage. This will require a valid monitoring network to be designed with additional bores required for adequate coverage of the hydrogeological conditions at the Josephville site. Further investigations would also be enhanced by undertaking pump testing to investigate hydrogeological properties in the aquifer.

Geological control of physiography in Southeast Queensland: A multi-scale analysis using GIS

The study reported here, constitutes a full review of the major geological events that have influenced the morphological development of the southeast Queensland region. Most importantly, it provides evidence that the region’s physiography continues to be geologically ‘active’ and although earthquakes are presently few and of low magnitude, many past events and tectonic regimes continue to be strongly influential over drainage, morphology and topography. Southeast Queensland is typified by highland terrain of metasedimentary and igneous rocks that are parallel and close to younger, lowland coastal terrain. The region is currently situated in a passive margin tectonic setting that is now under compressive stress, although in the past, the region was subject to alternating extensional and compressive regimes. As part of the investigation, the effects of many past geological events upon landscape morphology have been assessed at multiple scales using features such as the location and orientation of drainage channels, topography, faults, fractures, scarps, cleavage, volcanic centres and deposits, and recent earthquake activity. A number of hypotheses for local geological evolution are proposed and discussed. This study has also utilised a geographic information system (GIS) approach that successfully amalgamates the various types and scales of datasets used. A new method of stream ordination has been developed and is used to compare the orientation of channels of similar orders with rock fabric, in a topologically controlled approach that other ordering systems are unable to achieve. Stream pattern analysis has been performed and the results provide evidence that many drainage systems in southeast Queensland are controlled by known geological structures and by past geological events. The results conclude that drainage at a fine scale is controlled by cleavage, joints and faults, and at a broader scale, large river valleys, such as those of the Brisbane River and North Pine River, closely follow the location of faults. These rivers appear to have become entrenched by differential weathering along these planes of weakness. Significantly, stream pattern analysis has also identified some ‘anomalous’ drainage that suggests the orientations of these watercourses are geologically controlled, but by unknown causes. To the north of Brisbane, a ‘coastal drainage divide’ has been recognized and is described here. The divide crosses several lithological units of different age, continues parallel to the coast and prevents drainage from the highlands flowing directly to the coast for its entire length. Diversion of low order streams away from the divide may be evidence that a more recent process may be the driving force. Although there is no conclusive evidence for this at present, it is postulated that the divide may have been generated by uplift or doming associated with mid-Cenozoic volcanism or a blind thrust at depth. Also north of Brisbane, on the D’Aguilar Range, an elevated valley (the ‘Kilcoy Gap’) has been identified that may have once drained towards the coast and now displays reversed drainage that may have resulted from uplift along the coastal drainage divide and of the D’Aguilar blocks. An assessment of the distribution and intensity of recent earthquakes in the region indicates that activity may be associated with ancient faults. However, recent movement on these faults during these events would have been unlikely, given that earthquakes in the region are characteristically of low magnitude. There is, however, evidence that compressive stress is building and being released periodically and ancient faults may be a likely place for this stress to be released. The relationship between ancient fault systems and the Tweed Shield Volcano has also been discussed and it is suggested here that the volcanic activity was associated with renewed faulting on the Great Moreton Fault System during the Cenozoic. The geomorphology and drainage patterns of southeast Queensland have been compared with expected morphological characteristics found at passive and other tectonic settings, both in Australia and globally. Of note are the comparisons with the East Brazilian Highlands, the Gulf of Mexico and the Blue Ridge Escarpment, for example. In conclusion, the results of the study clearly show that, although the region is described as a passive margin, its complex, past geological history and present compressive stress regime provide a more intricate and varied landscape than would be expected along typical passive continental margins. The literature review provides background to the subject and discusses previous work and methods, whilst the findings are presented in three peer-reviewed, published papers. The methods, hypotheses, suggestions and evidence are discussed at length in the final chapter.

How useful is expert opinion for predicting the distribution of a species within and beyond the region of expertise? A case study using brush-tailed rock-wallabiesPetrogale penicillata

1. Species' distribution modelling relies on adequate data sets to build reliable statistical models with high predictive ability. However, the money spent collecting empirical data might be better spent on management. A less expensive source of species' distribution information is expert opinion. This study evaluates expert knowledge and its source. In particular, we determine whether models built on expert knowledge apply over multiple regions or only within the region where the knowledge was derived. 2. The case study focuses on the distribution of the brush-tailed rock-wallaby Petrogale penicillata in eastern Australia. We brought together from two biogeographically different regions substantial and well-designed field data and knowledge from nine experts. We used a novel elicitation tool within a geographical information system to systematically collect expert opinions. The tool utilized an indirect approach to elicitation, asking experts simpler questions about observable rather than abstract quantities, with measures in place to identify uncertainty and offer feedback. Bayesian analysis was used to combine field data and expert knowledge in each region to determine: (i) how expert opinion affected models based on field data and (ii) how similar expert-informed models were within regions and across regions. 3. The elicitation tool effectively captured the experts' opinions and their uncertainties. Experts were comfortable with the map-based elicitation approach used, especially with graphical feedback. Experts tended to predict lower values of species occurrence compared with field data. 4. Across experts, consensus on effect sizes occurred for several habitat variables. Expert opinion generally influenced predictions from field data. However, south-east Queensland and north-east New South Wales experts had different opinions on the influence of elevation and geology, with these differences attributable to geological differences between these regions. 5. Synthesis and applications. When formulated as priors in Bayesian analysis, expert opinion is useful for modifying or strengthening patterns exhibited by empirical data sets that are limited in size or scope. Nevertheless, the ability of an expert to extrapolate beyond their region of knowledge may be poor. Hence there is significant merit in obtaining information from local experts when compiling species' distribution models across several regions.