The importance of ecological scale for wildlife conservation in naturally fragmented environments: A case study of the Brush-Tailed Rock-Wallaby (Petrogale Penicillata)

Determining the ecologically relevant spatial scales for predicting species occurrences is an important concept when determining species–environment relationships. Therefore species distribution modelling should consider all ecologically relevant spatial scales. While several recent studies have addressed this problem in artificially fragmented landscapes, few studies have researched relevant ecological scales for organisms that also live in naturally fragmented landscapes. This situation is exemplified by the Australian rock-wallabies’ preference for rugged terrain and we addressed the issue of scale using the threatened brush-tailed rock-wallaby (Petrogale penicillata) in eastern Australia. We surveyed for brush-tailed rock-wallabies at 200 sites in southeast Queensland, collecting potentially influential site level and landscape level variables. We applied classification trees at either scale to capture a hierarchy of relationships between the explanatory variables and brush-tailed rock-wallaby presence/absence. Habitat complexity at the site level and geology at the landscape level were the best predictors of where we observed brush-tailed rock-wallabies. Our study showed that the distribution of the species is affected by both site scale and landscape scale factors, reinforcing the need for a multi-scale approach to understanding the relationship between a species and its environment. We demonstrate that careful design of data collection, using coarse scale spatial datasets and finer scale field data, can provide useful information for identifying the ecologically relevant scales for studying species–environment relationships. Our study highlights the need to determine patterns of environmental influence at multiple scales to conserve specialist species such as the brush-tailed rock-wallaby in naturally fragmented landscapes.

An ecological assessment of secondary poisoning risk in the Australian sugarcane industry

Rodenticide use in agriculture can lead to the secondary poisoning of avian predators. Currently the Australian sugarcane industry has two rodenticides, Racumin® and Rattoff®, available for in-crop use but, like many agricultural industries, it lacks an ecologically-based method of determining the potential secondary poisoning risk the use of these rodenticides poses to avian predators. The material presented in this thesis addresses this by: a. determining where predator/prey interactions take place in sugar producing districts; b. quantifying the amount of rodenticide available to avian predators and the probability of encounter; and c. developing a stochastic model that allows secondary poisoning risk under various rodenticide application scenarios to be investigated. Results demonstrate that predator/prey interactions are highly constrained by environmental structure. Rodents used crops that provided high levels of canopy cover and therefore predator protection and poorly utilised open canopy areas. In contrast, raptors over-utilised areas with low canopy cover and low rodent densities, but which provided high accessibility to prey. Given this pattern of habitat use, and that industry baiting protocols preclude rodenticide application in open canopy crops, these results indicate that secondary poisoning can only occur if poisoned rodents leave closed canopy crops and become available for predation in open canopy areas. Results further demonstrate that after in-crop rodenticide application, only a small proportion of rodents available in open areas are poisoned and that these rodents carry low levels of toxicant. Coupled with the low level of rodenticide use in the sugar industry, the high toxic threshold raptors have to these toxicants and the low probability of encountering poisoned rodents, results indicate that the risk of secondary poisoning events occurring is minimal. A stochastic model was developed to investigate the effect of manipulating factors that might influence secondary poisoning hazard in a sugarcane agro-ecosystem. These simulations further suggest that in all but extreme scenarios, the risk of secondary poisoning is also minimal. Collectively, these studies demonstrate that secondary poisoning of avian predators associated with the use of the currently available rodenticides in Australian sugar producing districts is minimal. Further, the ecologically-based method of assessing secondary poisoning risk developed in this thesis has broader applications in other agricultural systems where rodenticide use may pose risks to avian predators.

Reading the environment : narrative constructions of ecological subjectivities in Australian children's literature

Ways in which humans engage with the environment have always provided a rich source of material for writers and illustrators of Australian children's literature. Currently, readers are confronted with a multiplicity of complex, competing and/or complementing networks of ideas, theories and emotions that provide narratives about human engagement with the environment at a particular historical moment. This study, entitled Reading the Environment: Narrative Constructions of Ecological Subjectivities in Australian Children's Literature, examines how a representative sample of Australian texts (19 picture books and 4 novels for children and young adults published between 1995 and 2006) constructs fictional ecological subjects in the texts, and offers readers ecological subject positions inscribed with contemporary environmental ideologies. The conceptual framework developed in this study identifies three ideologically grounded positions that humans may assume when engaging with the environment. None of these positions clearly exists independently of any other, nor are they internally homogeneous. Nevertheless they can be categorised as: (i) human dominion over the environment with little regard for environmental degradation (unrestrained anthropocentrism); (ii) human consideration for the environment driven by understandings that humans need the environment to survive (restrained anthropocentrism); and (iii) human deference towards the environment guided by understandings that humans are no more important than the environment (ecocentrism). iv The transdisciplinary methodological approach to textual analysis used in this thesis draws on ecocriticism, narrative theories, visual semiotics, ecofeminism and postcolonialism to discuss the difficulties and contradictions in the construction of the positions offered. Each chapter of textual analysis focuses on the construction of subjectivities in relation to one of the positions identified in the conceptual framework. Chapter 5 is concerned with how texts highlight the negative consequences of human dominion over the environment, or, in the words of this study, living with ecocatastrophe. Chapter 6 examines representations of restrained anthropocentrism in its contemporary form, that is, sustainability. Chapter 7 examines representations of ecocentrism, a radical position with inherent difficulties of representation. According to the analysis undertaken, the focus texts convey the subtleties and complexities of human engagement with the environment and advocate ways of viewing and responding to contemporary unease about the environment. The study concludes that these ways of viewing and responding conform to and/or challenge dominant socio-cultural and political-economic opinions regarding the environment. This study, the first extended work of its kind, makes an original contribution to ecocritical study of Australian children's literature. By undertaking a comprehensive analysis of how texts for children represent human engagement with the environment at a time when important environmental concerns pose significant threats to human existence, I hope to contribute new knowledge to an area of children's literature research that to date has been significantly under-represented.

Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Integrated Bayesian network frameworks for modelling complex ecological issues

Ecological problems are typically multi faceted and need to be addressed from a scientific and a management perspective. There is a wealth of modelling and simulation software available, each designed to address a particular aspect of the issue of concern. Choosing the appropriate tool, making sense of the disparate outputs, and taking decisions when little or no empirical data is available, are everyday challenges facing the ecologist and environmental manager. Bayesian Networks provide a statistical modelling framework that enables analysis and integration of information in its own right as well as integration of a variety of models addressing different aspects of a common overall problem. There has been increased interest in the use of BNs to model environmental systems and issues of concern. However, the development of more sophisticated BNs, utilising dynamic and object oriented (OO) features, is still at the frontier of ecological research. Such features are particularly appealing in an ecological context, since the underlying facts are often spatial and temporal in nature. This thesis focuses on an integrated BN approach which facilitates OO modelling. Our research devises a new heuristic method, the Iterative Bayesian Network Development Cycle (IBNDC), for the development of BN models within a multi-field and multi-expert context. Expert elicitation is a popular method used to quantify BNs when data is sparse, but expert knowledge is abundant. The resulting BNs need to be substantiated and validated taking this uncertainty into account. Our research demonstrates the application of the IBNDC approach to support these aspects of BN modelling. The complex nature of environmental issues makes them ideal case studies for the proposed integrated approach to modelling. Moreover, they lend themselves to a series of integrated sub-networks describing different scientific components, combining scientific and management perspectives, or pooling similar contributions developed in different locations by different research groups. In southern Africa the two largest free-ranging cheetah (Acinonyx jubatus) populations are in Namibia and Botswana, where the majority of cheetahs are located outside protected areas. Consequently, cheetah conservation in these two countries is focussed primarily on the free-ranging populations as well as the mitigation of conflict between humans and cheetahs. In contrast, in neighbouring South Africa, the majority of cheetahs are found in fenced reserves. Nonetheless, conflict between humans and cheetahs remains an issue here. Conservation effort in South Africa is also focussed on managing the geographically isolated cheetah populations as one large meta-population. Relocation is one option among a suite of tools used to resolve human-cheetah conflict in southern Africa. Successfully relocating captured problem cheetahs, and maintaining a viable free-ranging cheetah population, are two environmental issues in cheetah conservation forming the first case study in this thesis. The second case study involves the initiation of blooms of Lyngbya majuscula, a blue-green algae, in Deception Bay, Australia. L. majuscula is a toxic algal bloom which has severe health, ecological and economic impacts on the community located in the vicinity of this algal bloom. Deception Bay is an important tourist destination with its proximity to Brisbane, Australia’s third largest city. Lyngbya is one of several algae considered to be a Harmful Algal Bloom (HAB). This group of algae includes other widespread blooms such as red tides. The occurrence of Lyngbya blooms is not a local phenomenon, but blooms of this toxic weed occur in coastal waters worldwide. With the increase in frequency and extent of these HAB blooms, it is important to gain a better understanding of the underlying factors contributing to the initiation and sustenance of these blooms. This knowledge will contribute to better management practices and the identification of those management actions which could prevent or diminish the severity of these blooms.

Adaptation of Sudanese refugees in an Australian context : investigating helps and hindrances

The present study investigates the experiences of Sudanese refugees by exploring the themes that characterise participants’ experiences in Sudan, en route, and at their Australian destination. In particular, the research identifies several factors that may be seen as ‘helps’ or ‘hindrances’ to Sudanese refugees’ adaptation. Participants were 12 Sudanese refugees aged between 19 and 40 years who had been residing in Australia for five years or less. A qualitative phenomenological approach to data collection and analysis was employed. Examination of the interview transcripts revealed that all participants identified both ‘hindrances’ and ‘helps’ toward adaptation and indicated that positive adaptation is not only possible, but probable for Sudanese refugees in spite of their past experiences of trauma and present resettlement difficulties. Several practical implications were elicited from the research including a need for programs that actively promote refugees’ adaptation by encouraging the broadening of social networks.

Bacterial proteases from the intracellular vacuole niche ; protease conservation and adaptation for pathogenic advantage

Proteases with important roles for bacterial pathogens which specifically reside within intracellular vacuoles are frequently homologous to those which have important virulence functions for other bacteria. Research has identified that some of these conserved proteases have evolved specialised functions for intracellular vacuole residing bacteria. Unique proteases with pathogenic functions have also been described from Chlamydia, Mycobacteria, and Legionella. These findings suggest that there are further novel functions for proteases from these bacteria which remain to be described. This review summarises recent findings of novel protease functions from the intracellular human pathogenic bacteria which reside exclusively in vacuoles.

Reading the play : adaptation by prediction of agent motion

An adaptive agent improves its performance by learning from experience. This paper describes an approach to adaptation based on modelling dynamic elements of the environment in order to make predictions of likely future state. This approach is akin to an elite sports player being able to “read the play”, allowing for decisions to be made based on predictions of likely future outcomes. Modelling of the agent‟s likely future state is performed using Markov Chains and a technique called “Motion and Occupancy Grids”. The experiments in this paper compare the performance of the planning system with and without the use of this predictive model. The results of the study demonstrate a surprising decrease in performance when using the predictions of agent occupancy. The results are derived from statistical analysis of the agent‟s performance in a high fidelity simulation of a world leading real robot soccer team.

Building climate change resilience and adaptive capacity in Australia’s community sector using social media and technology innovation

Public and private sector organisations worldwide are putting strategies in place to manage the commercial and operational risks of climate change. However, community organisations are lagging behind in their understanding and preparedness, despite them being among the most exposed to the effects of climate change impacts and regulation. This poster presents a proposal for a multidisciplinary study that addresses this issue by developing, testing and applying a novel climate risk assessment methodology that is tailored to the needs of Australia’s community sector and its clients. Strategies to mitigate risks and build resilience and adaptive capacity will be identified including new opportunities afforded by urban informatics, social media, and technologies of scale making.

RAP-A Indigenous supplement : guidelines for the adaptation and implementation of the RAP Program for indigenous adolescents

The RAP-A Indigenous supplement has been designed to provide guidelines for the Adaptation and implementation of the RAP Program for indigenous adolescents. It describes a variety of adaptations that have been made to RAP-A to make it more suitable for indigenous teenagers.

Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.

Predicting loss and fragmentation of habitat of the vulnerable subtropical rainforest tree Macadamia integrifolia with models developed from compiled ecological data

Habitat models are widely used in ecology, however there are relatively few studies of rare species, primarily because of a paucity of survey records and lack of robust means of assessing accuracy of modelled spatial predictions. We investigated the potential of compiled ecological data in developing habitat models for Macadamia integrifolia, a vulnerable mid-stratum tree endemic to lowland subtropical rainforests of southeast Queensland, Australia. We compared performance of two binomial models—Classification and Regression Trees (CART) and Generalised Additive Models (GAM)—with Maximum Entropy (MAXENT) models developed from (i) presence records and available absence data and (ii) developed using presence records and background data. The GAM model was the best performer across the range of evaluation measures employed, however all models were assessed as potentially useful for informing in situ conservation of M. integrifolia, A significant loss in the amount of M. integrifolia habitat has occurred (p < 0.05), with only 37% of former habitat (pre-clearing) remaining in 2003. Remnant patches are significantly smaller, have larger edge-to-area ratios and are more isolated from each other compared to pre-clearing configurations (p < 0.05). Whilst the network of suitable habitat patches is still largely intact, there are numerous smaller patches that are more isolated in the contemporary landscape compared with their connectedness before clearing. These results suggest that in situ conservation of M. integrifolia may be best achieved through a landscape approach that considers the relative contribution of small remnant habitat fragments to the species as a whole, as facilitating connectivity among the entire network of habitat patches.