Lian Yeap

Wildlife health data can be a powerful contributor to conservation outcomes, disease surveillance, and the broader objectives of One Health – an aim to achieve optimal health for people, animals, and the environment. Collections of wildlife necropsy reports are a common source of such data. However, the nature of these data creates a resource barrier between acquisition and analysis, resulting in sporadic extraction to inform such outcomes. To evaluate challenges and opportunities provided by wildlife health data, necropsy records for all the culturally, economically, and ecologically significant Sphenisciformes within the Wildbase Pathology Register of Aotearoa New Zealand were extracted, validated, and analysed. This manual process highlighted the dominance of a threatened and arguably cryptic species in the database (hoiho or yellow eyed penguin, Megadyptes antipodes), and that infectious/ inflammatory diagnoses were the most frequently encountered across all reviewed reports (35.7%, 523/1463). The free-text nature of many fields complicated analysis through high rates of typographical variance requiring manual resolution. The manual review shed light on threats to Sphenisciformes in Aotearoa, but also highlighted the temporal cost of knowledge extraction. Using these insights, an application was developed to facilitate time sensitive knowledge extraction, via text-mining and a dashboard approach to analyse and display information akin to the manual necropsy review. Simple algorithms were used to derive categorical fields such as species, and sex, while more complex query-based algorithms were used to quantify subjective elements, such as the prevalence of specific clinicopathologic findings. To evaluate the performance of this application nine professionals in wildlife health were recruited to a pilot study, to quantify the occurrence of four clinicopathological findings across two species datasets extracted from the Wildbase Pathology Register. Results from the testers were compared to the manual review (a “gold standard”), to determine the proportion of false negative and false positive records returned by each tester across the four clinicopathological findings that had been assigned to find. Mean F1-scores, which infer the level of agreement between the tester and the manual review, ranged from 0.63-0.93. Agreement was affected by tester, and the clinicopathologic finding being examined. The majority of misclassification (false positive or false negative records) was attributed to inappropriate search term selection and differences in interpretation of records. Further, the linguistically simple clinicopathologic findings (e.g., ‘oiled’) performed more consistently across users and in greater agreement with the manual review when compared to the other findings tested. The value of the application was affirmed in the pilot testing, however highlighted the potential for individual users, and clinicopathological findings with high rates of synonymy (e.g., “Starvation”), to impact performance. Overall, the development and testing of this application demonstrates the under-recognised value of automated methods in the extraction of knowledge from painstakingly acquired wildlife health data. This utility may be improved through the implementation of more sophisticated semantic-based techniques for data extraction as compared to the relatively simple term-based approaches utilised here. With early warning a recognised precursor to the success of any intervention, be it for conservation or infectious disease purposes, approaches that fast-track evidence-based adaptive management are a global priority for wildlife health.

The south-west of Western Australia (SWWA) is home to three species of threatened endemic black cockatoos. Anthropogenic activities including urbanisation and agriculture have led to the loss of at least 70% of pre-colonial native vegetation and much of what remains exists in a highly fragmented state within a matrix of human modified landscapes. The black cockatoos of SWWA interact in varying degrees with these modified landscapes, with consequences to fitness that are largely unknown.

In this project, I used modern tracking technologies to study the ecology of Carnaby’s cockatoo (CC) and the forest red-tailed black cockatoo (FRBC) in modified habitats. Using GPS units with integrated accelerometer devices, I gained insight into the fine-scale habitat use of these birds, as well as informing the interaction between habitat, behaviour, and energy expenditure. In addition, I analysed foraging resources for energetic content to further inform patterns of activity revealed by tracking data.

FRBC were tracked in both their natural forest habitat and the urban environment into which they have recently expanded. Urban birds were found to expend 25% more energy per day, with little evidence that this was adequately offset by foraging on exotic foods of higher calorific value. CC were also tracked in the urban area where birds spending more 􀆟me utilising the smallest fragments of remnant vegetation were found to travel significantly further each day. Daily distance travelled was in turn associated with greater energetic expenditure. Breeding CCs were tracked in the wheatbelt where the recent introduction of canola to the diet has been associated with improved reproductive outcomes. The existence of an upper limit to canola foraging was discovered, even when high temperatures reduced time available for foraging on native vegetation.

The research undertaken for this thesis has added to our understanding of the ecology of both species and the fitness consequences imposed on each by interaction with modified landscapes. The information herein will contribute to the conservation of Carnaby’s cockatoos and forest red-tailed black cockatoos by directly informing their respective Recovery Plans.

The aim of this project was to determine the prevalence of bornavirus, nidovirus, sunshinevirus and Mycoplasma spp. in pythons in Western Australia. Two captive cohorts were screened: snakes which had been confiscated by the Department of Biodiversity Conservation and Attractions (DBCA) (n=38) and snakes from Perth Zoo (n=15), for which longitudinal samples were also available for all 15 individuals for 2015 and 2017. A third cohort comprised free-living pythons captured and sampled from various locations within Western Australia (n=17). The majority of the pythons in the study were Antaresia spp., Morelia spp. and Aspidites spp.

Deep oesophageal, oral and cloacal swabs, and blood samples were collected. The swabs were screened using conventional and/or quantitative Polymerase Chain Reaction (PCR). Where relevant, positive amplicons were sequenced.

Sunshinevirus and bornavirus were not detected in any of the pythons sampled in this study. All pythons from Perth Zoo tested negative for nidovirus. Two pythons from the confiscated cohort (5.3%; 95% CI: 0.6%, 17.7%) were positive for nidovirus. All of the free-living pythons tested negative for nidovirus, with the exception of one individual which had inconclusive results. Sampling confirmed that Mycoplasma spp. were present in all three cohorts. The highest rates of Mycoplasma spp. detection occurred within the Perth Zoo cohort in 2015 (73.3%; 95% CI: 44.9%, 92.2%) and 2017 (86.7%; 95% CI: 58.5%, 98.3%) followed by the confiscated population (52.6%; 95% CI: 35.8%, 69.0%), and finally the free-living population (35.3%; 95% CI:14.2%, 61.7%). Mycoplasma spp. were detected in snakes with a range of clinical examination findings, with the majority in clinically normal individuals. Additional studies are necessary to determine the clinical significance of Mycoplasma spp. in snakes. This research is one of only a few studies reporting virology and bacteriology screening in free-living pythons in Australia, and is the first report of Mycoplasma spp. detection in freeliving Australian python species.

The current state of sea turtle health in the Indian Ocean is largely unknown, especially for the endemic flatback turtle (Natator depressus) which is listed as ‘vulnerable’ in Western Australia (WA) and ‘data deficient’ globally. Anecdotally, the causes of illness, injury, and death in Western Australian turtles are comparable to those in other parts of Australia and the world (e.g., spirorchiidiasis, fibropapillomatosis, and marine debris interaction) but scientific studies to validate these reports are particularly limited in this region. To address these knowledge gaps, causes of both live and dead turtle strandings in WA were investigated through an array of veterinary diagnostic techniques including necropsy, clinical pathology, diagnostic imaging, histopathology, parasitology, microbiology, toxicology, and molecular analyses. Health assessments were conducted on live animals to determine baseline levels of health and disease for specific populations, predominately nesting and foraging flatback turtles.

Through these health and disease investigations, baselines were developed, along with the discovery of new diseases in flatback turtles including a novel haemoparasite, Haemocystidium spp., occurring specifically in the foraging life stage; a potentially emerging zoonotic bacterium, Streptococcus iniae associated with a multi-species mass mortality event involving post-hatchlings; as well as spirorchiidiasis, previously unreported in this species. Other unusual and emerging diseases were also reported in sea turtles in this study, including microsporidial myopathy, salt gland adenitis, gout, and pseudogout.

In this study, natural disease-related causes of mortality occurred more frequently than direct anthropogenic causes, with parasitoses the most frequently occurring natural disease. Spirorchiidiaisis was the most common cause of mortality (32.0%) with a prevalence of 93.2% in turtles susceptible to the disease (i.e., excluding the post-hatchling life stage). The next most common cause of mortality was unknown (17.3%), followed by trauma (13.3%), endoparasitosis (10.7%), infectious disease (6.7%), and pneumonia (6.7%), with the remaining mortality categories each accounting for less than 5% of cases (including systemic inflammation, osmoregulatory disorder, gastrointestinal impaction, gastrointestinal foreign body, fibropapillomatosis, and metabolic disorder).

We developed the first flatback turtle reference intervals (RIs) in Reference Value Advisor (RefVal v2.1) following the American Society of Veterinary Clinical Pathology (ASVCP) guidelines. We found flatback turtle RIs were generally similar to other published sea turtle RIs and reference values (RVs) but detected significant differences in our study for the various boundary conditions including life stage (nesting or foraging), as well for measurement methodology (field or laboratory tests), justifying the establishment of separate RIs/RVs for nesting and foraging flatbacks, and for field and laboratory techniques.

This study was the first sea turtle health and disease investigation in WA and the eastern Indian Ocean to offer broader insights into sea turtle health and disease status on a regional scale. These essential baselines provided a number of crucial functions which include serving as a reference point for future studies to monitor changes in population health and disease levels. Specifically, these baseline data will be useful for future comparative studies of the same population where changes are an indication of a changing environment. The blood RIs can be used for disease diagnosis, monitoring progress and assessing prognosis of clinical flatback turtle cases in rehabilitation. Considering that diseases in the marine environment are predicted to rise with increasing anthropogenic pressures, detection of new and emerging diseases is of significance to the global knowledge of sea turtle diseases; and for understanding and mitigating disease threats to sea turtle populations. Finally, this study provided a framework to integrate health into future conservation management decisions to ensure the long-term survival of sea turtles.

Historically it has been difficult to gain information on the movement ecology of psittacine species in Australia. Using a novel double-tagging telemetry method, this research, aimed to: investigate regional differences in movement of the three black cockatoo species endemic to Western Australia; identify key roost and foraging sites for these species across regions; and estimate home range sizes for flocks in resident areas, using a combination of GPS and satellite PTT tags.

Tagged birds served as markers of flock movement once integrated into a wild flock of conspecifics, which was confirmed through means of behavioural change point analysis and field observations. Linear mixed models were used to determine differences in movement across regions, revisitation analysis was used to identify key habitat sites, and an auto-corrected Kernel density estimator was used to estimate the home ranges.

Results showed that key roosts sites for the three species predominantly occurred on public green space and private property. These were closely associated with foraging habitat which mainly occurred as remnant vegetation in the landscape or as nature reserves. Riparian zones and roadside vegetation were shown to play a crucial role as foraging habitat and in providing connective landscape structures. Daily movement distances differed both between and within regions depending on habitat matrix, resulting in varying home range sizes. These results suggest that movement for the three black cockatoo species is region specific, driven by food resources in the landscape. In addition, between species, movement varied as each species uses the landscape in different ways, depending on seasonal movements and ecological requirements.

This research has provided critical baseline data required to address knowledge gaps listed in Recovery Plans for these species of black cockatoo. Further research is now required to include these data in resource and habitat selection models to identify how the landscape matrix affects movement, which will facilitate adaptive habitat management and conservation plans for black cockatoos in Western Australia.

Lumpy jaw is a well-recognised cause of morbidity and mortality in captive macropods (Macropodidae) worldwide. The extent and causes of the disease are largely unknown, although multiple risk factors associated with a captive environment are thought to contribute to the development of clinical disease. Identification of risk factors associated with lumpy jaw would assist with the development of preventive management strategies, potentially reducing mortalities.

A cross-sectional study was undertaken from 2011 to 2015, to determine prevalence and risk factors for this disease through the distribution of a survey to 527 institutions across Australia and Europe; two regions where macropods are popular exhibits. Veterinary and husbandry records from the period 1st January 1995 up to and including 28th November 2016 (the last date when data were extracted from zoo records) were analysed in a retrospective cohort study, examining risk factors for developing disease and treatments used, over time. Computed tomography was used to examine disease occurrence in wild macropods using skulls from population management culls.

The prevalence of lumpy jaw was found to differ between the two regions (p < 0.0002). A review of 6178 records for 2759 macropods housed within eight zoos across the Australian and European regions, found incidence rates and risk of infection differed between geographic regions and individual institutions. Risk of developing lumpy jaw increased with age, particularly for macropods >10 years (Australia IRR 7.63, p < 0.001; Europe IRR 7.38, p < 0.001). Treatment approach varied and prognosis was typically poor with 62.5% mortality for Australian and European regions combined. Lumpy jaw was detected in all captive genera examined, but was absent from the wild populations studied.

Geographic region influenced the incidence of lumpy jaw, the risks associated with developing clinical disease, and preferred treatment approach. Despite advances in antibiotic therapy and surgical techniques, treatment of lumpy jaw is largely unrewarding for the individual and should be approached on an individual basis. This research provides new information about this refractory disease and makes practical recommendations to reduce disease risk. This information may assist institutions in providing optimal long-term health management for captive macropods; such efforts having a positive impact on both welfare and conservation, including but not limited to captive breeding and translocation programs.

This field trip has a One Heath focus and is a collaborative initiative between Murdoch University School of Veterinary Medicine, Nature Travel Namibia, the Cheetah Conservation Fund (CCF), Naankuse and other wildlife organisations. Trip activities include lecture sessions on wildlife conservation, one health, human-wildlife conflict, theory and practical sessions on wildlife management and capture and experiencing the amazing wildlife and ecosystems of Etosha National Park.

The trip can be counted as a placement for VET 645 Advanced Practice in Wildlife, Zoological and Conservation Medicine or as EME experience

Advanced Practice in Wildlife, Zoological and Conservation Medicine provides focused study in the disciplines of Wildlife, Zoological and Conservation Medicine. Students will have the opportunity to extend their theoretical knowledge and develop practical skills and professional competence beyond the minimum standards required for graduation and registration.

This unit provides training in Wildlife Medicine necessary to deal with sick and injured wild fauna and non-domestic companion animals which could be presented for examination and treatment to veterinarians in private practice. It covers appropriate methods of physical and chemical restraint; diagnosis and treatment of common diseases and injuries; zoonoses; and nutrition and husbandry associated with management of wild fauna in captivity.

Conservation Medicine involves the integration of veterinary science, conservation biology and public health and explores the relationships between animal, human and ecosystem health, and how global environmental changes affect these relationships.

There is opportunity to consolidate formative experiences in building productive relationships and psychological resourcefulness, and developing professional commitment and skills in personal reflection.