Dissertations / Theses on the topic 'Bandicoot'

Almost half of the world's mammal extinctions in the last two hundred years have occurred in Australia (Short and Smith 1994). The western barred bandicoot Perameles bougainville is one of a suite of species that is currently threatened with extinction, surviving only on two islands in Shark Bay, Western Australia. Reintroduction has been used as a tool in conservation biology to assist in the recovery of threatened species, such as the western barred bandicoot. The aims of this project were to 1) successfully reintroduce and establish a free-ranging mainland population of the western barred bandicoot at Heirisson Prong, Shark Bay, 2) contribute information on the biology of the species, its interactions with introduced species, and its likelihood of persistence as a reintroduced population in the longer-term, and 3) to provide recommendations to assist future reintroductions of the species. The first reintroduction of the western barred bandicoot from surviving remnant island populations to the mainland, some 60 years after its apparent mainland extinction, was from Dorre Island to Heirisson Prong in 1995. Animals were translocated initially to a predator-free refuge on Heirisson Prong, and then subsequently released to the 12 km2 peninsula where introduced predators (foxes Vulpes vulpes and feral cats Felis catus) had been controlled, but European rabbits Oryctolagus cuniculus had not. Despite a small founder number and high mortality of free-range bandicoots in the presence of a low-density feral cat population, the bandicoot population successfully established. The reintroduced population of western barred bandicoots provided an opportunity to study the biology of the species, and to compare it with the remnant island populations and other species of Australian bandicoot. Many population parameters were similar between the island and mainland western barred bandicoot populations, as well as between the western barred bandicoot and other bandicoot species, suggesting that the habitat at the reintroduction site is suitable for long-term persistence of the population. However, there were some notable differences. The western barred bandicoot is the smallest extant species of bandicoot, with fewer young per litter than recorded for other bandicoot species, adult sex ratios were closer to parity, animals reached sexual maturity later, and it is the only species of bandicoot where females are larger than males. Home range size is larger also than recorded for other species. Some of these differences may be explained in part by trade-offs between island dwarfism, lactational pressures, and nest defence. The nesting biology of the western barred bandicoot was studied at Heirisson Prong, including during periods of high and low densities of rabbits. Individuals of the species constructed and utilised nests in a similar fashion to other species of Australian bandicoot, nesting amongst litter underneath shrubs. The western barred bandicoot appeared to favour particular shrub species, especially when vegetation condition was poor due to rabbit damage, but displayed flexibility in being able to construct nests under a variety of shrub species where at least some surface litter was present. Grasses were used in nest construction only when rabbit density was low. Nests appear important for protection against temperature extremes and diurnal predators. Vegetation exclosures around three of the shrub species most commonly used by the western barred bandicoot for nest sites (Acacia ligulata, A. tetragonophylla and Melaleuca cardiophylla) were used to examine the impact of rabbits on vegetation on Heirisson Prong. A high-density rabbit population over the summer of 1997/98 caused in a decrease in canopy cover and the death of mature A. ligulata. Subsequent rainfall and low-density rabbit populations allowed A. tetragonophylla shrubs to recover their former structure, and M. cardiophylla to recover, but not to the same degree. The flexibility of western barred bandicoots in use of nest materials and their omnivorous diet may enable the species to survive in the face of habitat modification by rabbits. Population viability analysis was used to examine future options for the recovery of the endangered western barred bandicoot. Biological data from the Dorre Island and Heirisson Prong populations were input to the computer simulation program VORTEX. The western barred bandicoot populations were modelled under a variety of scenarios to examine the possible effects of changes in carrying capacity, founder population size, inbreeding depression, and the occurrence of drought and cat predation as catastrophes, on the probability of population extinction. This analysis highlighted the need for eradication of feral cats, above all other management actions. Cat predation was particularly potent when it acted through high loss of juveniles, as well as adult bandicoots. Predator control is considered critical for the long-term persistence of reintroduced populations of the western barred bandicoot. This study documents the first reintroduction of the endangered western barred bandicoot to mainland Australia. The population had been extant for four years at the completion of data collection for this thesis, in late 1999 and for over eight years at the finalisation of this thesis in July 2004. The knowledge gained from the reintroduction was used to discuss management recommendations and future options for the recovery of the species. The primary concern for reintroductions of this, and other species of bandicoots, remains the control of introduced predators. For long-term persistence of small, isolated populations, such as those of the western barred bandicoot at Heirisson Prong and the Arid Recovery Project at Roxby Downs in South Australia, and the eastern barred bandicoot Perameles gunnii at a range of sites in Victoria, the complete eradication of introduced predators is essential.

Conservation efforts to prevent the extinction of the endangered western barred bandicoot Perameles bougainville (WBB) are currently hindered by a debilitating progressive papillomatosis and carcinomatosis syndrome. Now extinct on mainland Australia, wild populations of the WBB are known only to exist on Bernier and Dorre Islands in Shark Bay, Western Australia. This thesis describes and analyses the pathological (gross, histological, ultrastructural) and immunohistochemical features of a papillomatosis and carcinomatosis syndrome in the WBB. The detection and characterisation of a novel virus, the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), found in association with cutaneous and muco-cutaneous papillomas and carcinomas, is described. BPCV1 was found to exhibit genomic and morphological features of both the Papillomaviridae and the Polyomaviridae, and may represent the first member of a new family of viruses. The findings of this study provide evidence that BPCV1 is the causative agent of the papillomatosis and carcinomatosis syndrome. Clinical, pathological and molecular evidence of the syndrome and BPCV1 were found in the Bernier Island WBB population at Red Cliff and in captive populations comprising all or a proportion of founder WBBs from this site, but not at all in the WBB population on Dorre Island or Heirisson Prong. The papillomatosis and carcinomatosis syndrome in the western barred bandicoot is a pertinent example of a disease process hampering efforts to prevent the extinction of an endangered species.

Conservation efforts to prevent the extinction of the endangered western barred bandicoot Perameles bougainville (WBB) are currently hindered by a debilitating progressive papillomatosis and carcinomatosis syndrome. Now extinct on mainland Australia, wild populations of the WBB are known only to exist on Bernier and Dorre Islands in Shark Bay, Western Australia. This thesis describes and analyses the pathological (gross, histological, ultrastructural) and immunohistochemical features of a papillomatosis and carcinomatosis syndrome in the WBB. The detection and characterisation of a novel virus, the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), found in association with cutaneous and muco-cutaneous papillomas and carcinomas, is described. BPCV1 was found to exhibit genomic and morphological features of both the Papillomaviridae and the Polyomaviridae, and may represent the first member of a new family of viruses. The findings of this study provide evidence that BPCV1 is the causative agent of the papillomatosis and carcinomatosis syndrome. Clinical, pathological and molecular evidence of the syndrome and BPCV1 were found in the Bernier Island WBB population at Red Cliff and in captive populations comprising all or a proportion of founder WBBs from this site, but not at all in the WBB population on Dorre Island or Heirisson Prong. The papillomatosis and carcinomatosis syndrome in the western barred bandicoot is a pertinent example of a disease process hampering efforts to prevent the extinction of an endangered species.

Conservation efforts to prevent the extinction of the endangered western barred bandicoot Perameles bougainville (WBB) are currently hindered by a debilitating progressive papillomatosis and carcinomatosis syndrome. Now extinct on mainland Australia, wild populations of the WBB are known only to exist on Bernier and Dorre Islands in Shark Bay, Western Australia. This thesis describes and analyses the pathological (gross, histological, ultrastructural) and immunohistochemical features of a papillomatosis and carcinomatosis syndrome in the WBB. The detection and characterisation of a novel virus, the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), found in association with cutaneous and muco-cutaneous papillomas and carcinomas, is described. BPCV1 was found to exhibit genomic and morphological features of both the Papillomaviridae and the Polyomaviridae, and may represent the first member of a new family of viruses. The findings of this study provide evidence that BPCV1 is the causative agent of the papillomatosis and carcinomatosis syndrome. Clinical, pathological and molecular evidence of the syndrome and BPCV1 were found in the Bernier Island WBB population at Red Cliff and in captive populations comprising all or a proportion of founder WBBs from this site, but not at all in the WBB population on Dorre Island or Heirisson Prong. The papillomatosis and carcinomatosis syndrome in the western barred bandicoot is a pertinent example of a disease process hampering efforts to prevent the extinction of an endangered species.

Thesis (Ph. D.)--University of Sydney, 2005.
Title from title screen (viewed 19 May 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the Faculty of Science. Degree awarded 2005; thesis submitted 2004. Includes bibliographical references. Also available in print form.

Almost half of the world�s mammal extinctions in the last two hundred years have occurred in Australia (Short and Smith 1994). The western barred bandicoot Perameles bougainville is one of a suite of species that is currently threatened with extinction, surviving only on two islands in Shark Bay, Western Australia. Reintroduction has been used as a tool in conservation biology to assist in the recovery of threatened species, such as the western barred bandicoot. The aims of this project were to 1) successfully reintroduce and establish a free-ranging mainland population of the western barred bandicoot at Heirisson Prong, Shark Bay, 2) contribute information on the biology of the species, its interactions with introduced species, and its likelihood of persistence as a reintroduced population in the longer-term, and 3) to provide recommendations to assist future reintroductions of the species. The first reintroduction of the western barred bandicoot from surviving remnant island populations to the mainland, some 60 years after its apparent mainland extinction, was from Dorre Island to Heirisson Prong in 1995. Animals were translocated initially to a predator-free refuge on Heirisson Prong, and then subsequently released to the 12 km2 peninsula where introduced predators (foxes Vulpes vulpes and feral cats Felis catus) had been controlled, but European rabbits Oryctolagus cuniculus had not. Despite a small founder number and high mortality of free-range bandicoots in the presence of a low-density feral cat population, the bandicoot population successfully established. The reintroduced population of western barred bandicoots provided an opportunity to study the biology of the species, and to compare it with the remnant island populations and other species of Australian bandicoot. Many population parameters were similar between the island and mainland western barred bandicoot populations, as well as between the western barred bandicoot and other bandicoot species, suggesting that the habitat at the reintroduction site is suitable for long-term persistence of the population. However, there were some notable differences. The western barred bandicoot is the smallest extant species of bandicoot, with fewer young per litter than recorded for other bandicoot species, adult sex ratios were closer to parity, animals reached sexual maturity later, and it is the only species of bandicoot where females are larger than males. Home range size is larger also than recorded for other species. Some of these differences may be explained in part by trade-offs between island dwarfism, lactational pressures, and nest defence. The nesting biology of the western barred bandicoot was studied at Heirisson Prong, including during periods of high and low densities of rabbits. Individuals of the species constructed and utilised nests in a similar fashion to other species of Australian bandicoot, nesting amongst litter underneath shrubs. The western barred bandicoot appeared to favour particular shrub species, especially when vegetation condition was poor due to rabbit damage, but displayed flexibility in being able to construct nests under a variety of shrub species where at least some surface litter was present. Grasses were used in nest construction only when rabbit density was low. Nests appear important for protection against temperature extremes and diurnal predators. Vegetation exclosures around three of the shrub species most commonly used by the western barred bandicoot for nest sites (Acacia ligulata, A. tetragonophylla and Melaleuca cardiophylla) were used to examine the impact of rabbits on vegetation on Heirisson Prong. A high-density rabbit population over the summer of 1997/98 caused in a decrease in canopy cover and the death of mature A. ligulata. Subsequent rainfall and low-density rabbit populations allowed A. tetragonophylla shrubs to recover their former structure, and M. cardiophylla to recover, but not to the same degree. The flexibility of western barred bandicoots in use of nest materials and their omnivorous diet may enable the species to survive in the face of habitat modification by rabbits. Population viability analysis was used to examine future options for the recovery of the endangered western barred bandicoot. Biological data from the Dorre Island and Heirisson Prong populations were input to the computer simulation program VORTEX. The western barred bandicoot populations were modelled under a variety of scenarios to examine the possible effects of changes in carrying capacity, founder population size, inbreeding depression, and the occurrence of drought and cat predation as catastrophes, on the probability of population extinction. This analysis highlighted the need for eradication of feral cats, above all other management actions. Cat predation was particularly potent when it acted through high loss of juveniles, as well as adult bandicoots. Predator control is considered critical for the long-term persistence of reintroduced populations of the western barred bandicoot. This study documents the first reintroduction of the endangered western barred bandicoot to mainland Australia. The population had been extant for four years at the completion of data collection for this thesis, in late 1999 and for over eight years at the finalisation of this thesis in July 2004. The knowledge gained from the reintroduction was used to discuss management recommendations and future options for the recovery of the species. The primary concern for reintroductions of this, and other species of bandicoots, remains the control of introduced predators. For long-term persistence of small, isolated populations, such as those of the western barred bandicoot at Heirisson Prong and the Arid Recovery Project at Roxby Downs in South Australia, and the eastern barred bandicoot Perameles gunnii at a range of sites in Victoria, the complete eradication of introduced predators is essential.

This thesis investigates the process of habitat fragmentation and the spatial and temporal scales at which it occurs. Fragmentation has become an important topic in biogeography and conservation biology because of the impacts it has upon species??? distributions and biodiversity. Various definitions of fragmentation are available but in this research it is considered to be the disruption of continuity, either natural or human-induced in its origins and operative at multiple spatial scales. Using the distribution of the southern brown bandicoot Isoodon obesulus as a case study, three spatial scales of fragmentation were analysed. At the continental scale, the Australian distribution of the subspecies I. o. obesulus was examined in relation to climate, geology and vegetation cover at the time of European settlement of Australia and two centuries later. Using archived wildlife records and Geographic Information Systems (GIS) analyses, habitat suitability models were created to assess natural and human-induced fragmentation of the distribution of I. obesulus in 1788 and 1988. At the regional scale, a study was made of the distribution of I. obesulus in the south-east of the State of South Australia. Again, natural and human-induced patterns of habitat fragmentation were modelled using GIS with climate, soil and vegetation data for the time of European settlement and at present. At the local scale, the distribution of I. obesulus was the subject of a detailed field survey of 372 sites within 29 remnant patches of native vegetation in south-eastern South Australia in order to understand the variables that cause habitat fragmentation. Geographic information systems were used again but in a different way to carefully stratify the field survey by overlaying maps of topography, vegetation and past fires. The large dataset collected from the surveys was described using six generalized linear models which identified the significant variables that fragment the distribution of I. obesulus at a local scale. From the results of the field surveys, a subset of four remnants was chosen for further GIS spatial modelling of the probability of I. obesulus occurring within remnants in response to fire via a controlled burning programme put in place to reduce accumulating fuel loads. These investigations show that habitat fragmentation can be caused by different factors at different spatial scales. At the continental scale, it was found that climate played a dominant role in influencing the fragmented distribution of I. obesulus but vegetation change during the past two centuries has also had a profound impact on the availability of habitat. Within south-eastern South Australia, the species??? regional scale distribution is constrained by climate and also by soil and vegetation patterns. Dramatic change to its regional distribution occurred in the 20th century as a result of the clearance of native vegetation for planting pastures, crops and pines. Fragmentation at the regional scale has resulted in the remaining habitat being reduced to small, isolated, remnant patches of native vegetation. At the local scale it was found that variables which disrupt the continuity of I. obesulus habitat within remnants include vegetation cover in the 0-1 m stratum, abundance of Xanthorrhoea australis and soil texture. For a subset of sites located in one landsystem of the study area, named Young, the age of vegetation since it was last burnt was also found to be a significant variable, with vegetation 10-14 years old since burning providing the most suitable habitat. Spatial modelling of two scenarios for prescribed burning over 15 years revealed that the use of fire as a habitat enhancement tool will be complicated and require a detailed understanding of the factors that cause natural fragmentation in the distribution of I. obesulus at the local scale. A further conclusion of the study was that ecological relationships between species and their habitats require careful interpretation of multi-scaled datasets and conservation plans for endangered species ought to be made at multiple spatial scales. Future research directions are identified including the linking of multi-scaled habitat fragmentation models to genetic studies of the species throughout its range.

One of the few commonly occuring species of digging marsupial in south-western Australia is the subspecies of southern brown bandicoot (Isoodon obesulus fusciventor). Unlike a large proportion of Australian digging marsupials that have suffered attrition, bandicoots have persisted and shown resilience to human-mediated disturbance in peri-urban regions. This thesis evaluates some of the ecological roles of bandicoots in ecosystem processes in degraded Eucalyptus gomphocephala woodland in Yalgorup National Park. Bandicoots forage for the fruiting bodies of mycorrhizal fungi and other subterranean food and in doing so make small pits in the soil surface. Surveys of these foraging pits over a six month period revealed they are sites of lower soil hydrophobicity and higher soil moisture compared to the surrounding undisturbed soil. Additionally, the foraging pits and the area immediately surrounding them collect more leaf litter than the surrounding areas. The impact of foraging pits on ant-seed removal rates was explored by creating artificial diggings. Three local seed species Acacia saligna, Eucalyptus gomphocephala, and Kennedia prostrata were used in a cafeteria style experiment. Results found artificially created diggings had no effect on seed removal rates and that E. gomphocephala had the highest seed removal rate. This study suggests that bandicoots provide an important source of soil surface heterogeneity, contributing to ecosystem processes. Their presence in the landscape has the potential to contribute to the restoration of degraded ecosystems.

For more than a decade, community groups, scientific organizations and government agencies have collaborated to repopulate the endangered western barred bandicoot (Perameles bougainville). While initially successful, the unexpected discovery of a papillomatosis and carcinomatosis syndrome in captive and wild populations of P. bougainville exposed a dearth of knowledge regarding their diseases. This dissertation addresses this issue through study of the clinical pathology, immunology, parasitology, and virology of P. bougainville. To facilitate the detection and understanding of diseases in P. bougainville, guidelines for interpreting haematology and clinical chemistry results were developed, including calculated species-specific reference intervals for plasma aspartate transaminase activity (20–283 U/L), haemoglobin (122-165 g/L), haematocrit (0.36-0.49 L/L), total leukocytes (2.9-14.9 x10^9/L), monocytes (0-0.6 x10^9/L), eosinophils (0-0.9 x10^9/L) and total protein (47-63 g/L) estimated by refractometry. P. bougainville immunoglobulin was also fractionated from plasma and inoculated into sheep to derive antiserum for serological screening assays. Arthropods, helminths and protozoa parasitic on P. bougainville were catalogued and Eimeria kanyana n. sp. was formally described. The pathogenic and zoonotic potential of bacteria detected in ticks parasitic on P. bougainville was also considered. The association between bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) and the western barred bandicoot papillomatosis and carcinomatosis syndrome was investigated using PCR, in situ hybridization and virus isolation. Optimized in situ hybridization techniques demonstrated BPCV1 DNA within keratinocyte and sebocyte nuclei, and BPCV1 mRNA within the cytoplasm. BPCV1 virions were isolated by ultracentrifugation and visualized with negative stain transmission electron microscopy revealing icosahedral, non-enveloped viral capsids ~47 nm in diameter, comparable to viruses classified within Papillomaviridae and Polyomaviridae. A novel virus, tentatively named bandicoot papillomatosis carcinomatosis virus type 2 (BPCV2) was discovered in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus). It had a circular double-stranded DNA genome of 7277 bp, and encoded two papillomavirus-like structural proteins, L1 and L2, and two polyomavirus-like putative transforming proteins, large T antigen and small t antigen. DNA and RNA in situ hybridization confirmed the presence of BPCV2 nucleic acids within lesion biopsies. The discovery of the bandicoot papillomatosis carcinomatosis viruses has provoked reassessment of the established virus taxonomy paradigm, theories of virus-host co-speciation and bandicoot population management strategies.

Roads are primary agents of habitat fragmentation and transform landscapes on a global scale. Roads remove habitat and create barriers or filters to the movement of many wildlife species. Moreover, roads disrupt population processes by breaking up continuous populations into smaller, isolated subpopulations or metapopulations, which can suffer genetic drift and become more vulnerable to stochastic processes. Consequently, understanding and mitigating the impact of roads on wildlife has attracted increasing international interest in recent decades. Foremost in efforts to re-connect wildlife populations severed by roads has been the installation of crossing-structures. These are engineered structures designed to provide the opportunity for animals to safely cross either over the road (e.g. land-bridges, rope or wooden canopy-bridges) or under the road (e.g. underpasses, culverts, ecopipes). Crossing-structures enhance the permeability of roads to animal movement thereby improving the ‘functional connectivity’ of the surrounding landscape, or the degree to which the inter-fragment landscape (matrix) facilitates movement. Crossing-structures have thus become a common feature of new road projects in developed countries. Research into the efficacy of crossing-structures is very much in its infancy and has largely focused on assessing whether structures are being used by different wildlife species. As a consequence, we know very little about higher order questions pertaining to population processes, particularly whether the viability of local populations is enhanced by the deployment of crossing-structures. Furthermore, the deployment of crossing-structures has largely focused on terrestrial vertebrates and scant attention has been directed at mitigating road impacts on arboreal mammals, particularly gliding mammals (gliders). This thesis endeavours to address some of these information gaps by presenting the results of a number of investigations into wildlife use of road crossing-structures located in subtropical, eastern Australia. The topics of investigation include: i) glider use of wooden poles on a road land-bridge; ii) home-ranges of gliders residing near road crossing-structures; iii) modelling the effect of connecting habitat patches across road-gaps on glider metapopulation viability; and, vi) determining the effect of road widening on bandicoot use of highway underpasses. They represent the first studies of their kind to investigate such topics. The Australian squirrel glider Petaurus norfolcensis (Marsupialia: Diprotodontia) is a gliding marsupial distributed along the eastern seaboard of Australia. It is listed as threatened in the southern part of its geographic range due to habitat fragmentation. I investigated whether 7-m high wooden poles installed on a land-bridge could enable squirrel gliders to cross a road canopy-gap at two locations in Brisbane, the capital city of Queensland. This represented the first attempt in the world to facilitate road crossing by a gliding mammal in this way. At one location no road crossing was revealed from trapping over a 3-year period. Radio-tracking over 8 months revealed 3 occasions when animals whose home-ranges were aligned along the road had crossed the road. Hair-sampling devices revealed use of the poles at one location during 15 of 20 sampling sessions over a 3-year period, and at the second location during 6 of 6 sampling sessions over a 6-month period. Detection of hair on all poles during some sessions at both locations suggests complete crossings could occur. These observations suggest that wooden poles can be used to facilitate road-crossing by gliding mammals. Obtaining information on the use of novel road-crossing technologies such as gliding poles is a necessary first step to understanding their efficacy. However, the ultimate test of a crossing-structure’s effectiveness is in establishing to what extent has it alleviated the barrier effect of the road and prevented the extirpation of local populations. Accordingly, I utilised the population modelling program VORTEX to assess the viability of a metapopulation of squirrel gliders and Australia’s largest gliding marsupial, the greater glider (Petauroides volans), occurring in forest remnants in the fastest urbanising region of Australia. Population studies were conducted over two years within two of these forest remnants (one small, one large) connected across a major road by a land-bridge with gliding poles and rope canopy-bridges. Whereas I obtained direct evidence of squirrel glider use of the land-bridge poles, it is currently unknown whether greater gliders will use the crossing structures but available tree height and spacing do not allow a glide crossing and fences with metal flashing prevent access to the road by terrestrial and arboreal mammals. My modelling revealed that even a relatively low rate of dispersal facilitated by these structures would substantially reduce the probability of extirpation of the smaller subpopulation for both glider species. This rate of dispersal is plausible given the small distance involved (~50 m). The inclusion of wildfire as a catastrophe in my model suggests that these two remnants may encounter an undesirable level of extinction risk. This can be reduced to an acceptable level by including inter-patch movement via dispersal among other forest remnants. However, this requires connection to a very large remnant 8 km away, through a set of smaller remnants that straddle two motorways. These motorways create discontinuities in forest cover that are beyond the gliding ability of both these species and will require the deployment of crossing-structures to allow inter-patch movement. Whereas our knowledge of wildlife use of road crossing-structures has grown considerably in recent years, little is known about the effect that road widening may have on patterns of use by target fauna. To address this, I investigated the effect that duplicating a highway had on bandicoot (Marsupialia: Peramelemorphia) use of underpasses at Brunswick Heads in north east New South Wales (NSW). This study represented one of the first of its kind in Australia and spanned the period of pre and post-construction over an eight year period. Evidence from trapping data showed that individuals of the two bandicoot species present at the study site (i.e. Isoodon macrourus and Perameles nasuta) incorporated both sides of the road corridor into their home ranges and that the majority of movements were likely associated with foraging. The trapping data also demonstrated spatial overlap between and within sexes and congeners suggesting that underpasses were functionally available to resident animals and were each being used by multiple individuals. Despite this, gaining clear insights on the effect that road-widening had on underpass use by bandicoots was confounded by drought, loss of high quality habitat, a decline in bandicoot abundance, the presence of foxes and different design characteristics of new underpasses. Further surveys are required at Brunswick Heads to elucidate this issue. The results of my investigations on bandicoot and glider use of road crossing-structures provide strong support for the need to manage road impacts on wildlife at multiple scales. At the patch or site-level, a number of enhancements are required to improve the functionality of the investigated crossing-structures and to make the study sites more amenable to the target species. At the landscape-level, management needs to focus on improving functional connectivity in the surrounding landscape to strengthen the viability of local metapopulations. This will require the combination of habitat restoration works, wildfire control and the deployment of crossing structures where large roads and motorways breach forest cover. In the case of gliders, the deployment of crossing-structures can be achieved rapidly and cost-effectively by installing gliding poles along motorway edges and in median strips at locations where forest cover is breached. Future research at these study sites needs to continue for much longer periods (i.e. 5-10 years) and incorporate genetic techniques. This will assist in improving our understanding of the isolation effects of road barriers and whether or not gene flow is restored by the installation of crossing-structures. This should be routinely combined with viability assessments (e.g. PVA) to determine how populations are affected by roads and whether they might benefit from crossing structures. Research is also required to provide insights to dispersal behaviour, particularly for gliders, and the likely use of road-crossing structures. Loss of habitat and habitat connections is continuing in my study landscapes and this is likely to have dire consequences for wildlife if land managers are unable to retain appropriate habitat cover with corridors and install effective wildlife road crossing-structures where large roads bisect wildlife habitat.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

An increasing number of endangered species have reached the threshold prompting management decisions to commence captive breeding and reintroduction. Such intervention is costly and requires a substantial investment of resources that might otherwise be spent on alternate conservation options. It is important, therefore, that such measures make use of all available information to ensure the success of the reintroduction effort, not just in the short-term but also well into the future. The diverse range of elements to be considered include habitat factors, number and sex ratio of founders, number of populations to establish, source populations to use, timing of releases and the need to supplement the populations. All of these factors can benefit through input from molecular genetic data to improve the quality of information used in decision making. Levels of genetic variation are strongly correlated with population fitness and their potential for long-term persistence. For this thesis I examined levels of genetic diversity at neutral and functional regions of the genome for two endangered species of Australian marsupials: the western barred bandicoot, Perameles bougainville; and Queensland populations of the greater bilby, Macrotis lagotis. These two species are under threat from similar processes: habitat destruction and modification for agriculture; predation by foxes and feral cats; changes to traditional fire regimes and competition with introduced pest species. Since European settlement, P. bougainville has become extinct on the mainland and now exists on just two islands in Shark Bay, Western Australia. Macrotis lagotis has suffered a range contraction of over 80% and the Queensland population has become disjointed from other populations to the west. Reintroduction efforts are under way for both species but, until now, the projects have not made use of molecular genetic data to inform their management decisions. I have used marker systems from nuclear microsatellite DNA, mitochondrial control region DNA and the functionally important major histocompatability complex (MHC) to assess levels of genetic diversity in natural, captive and reintroduced populations of both species. DNA was sourced from ear-tissue for P. bougainville and from ear-tissue and faecal pellets for M. lagotis. The levels of microsatellite diversity for the two natural populations of P. bougainville (Bernier Island: HE = 0.27± 0.1, A = 1.8± 0.3; Dorre Island: HE = 0.31± 0.1, A = 2.2± 0.4) were low compared to other marsupials and significantly lower than that recorded for the natural Queensland population of M. lagotis (Astrebla Downs: HE = 0.76 ± 0.03, A = 4.31 ± 0.3). In all cases, the diversity of captive and reintroduced populations was reduced relative to their source populations except for the Dryandra captive population of P. bougainville (HE = 0.54± 0.1, A = 2.69± 0.2) which was founded following a mixed breeding strategy using individuals sourced from both natural island populations. Distribution of mtDNA haplotypes among geographical regions indicated that, for each species, populations could be combined in captive breeding programs without compromising distinct evolutionary lineages. Design of MHC assays proved difficult for M. lagotis, but for P. bougainville two separate MHC class II alleles were identified. These two alleles were fixed across all individuals in all populations suggesting that they may represent two paralogous loci in P. bougainville and that MHC diversity is unusually low for this species. I have recommended that the recovery programs for both species be expanded to incorporate regular monitoring of molecular data to ensure that genetic diversity is retained and maximised in all populations. Where possible, the natural populations should be maintained as “pure lines” to increase overall species genetic diversity but the captive and reintroduced populations should make use of supplementary individuals from a mixture of sources to maximise variation and thus the adaptive potential of these populations in the novel environments to which they are being introduced.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Faculty of Science, Environment, Engineering and Technology
Full Text

For more than a decade, community groups, scientific organizations and government agencies have collaborated to repopulate the endangered western barred bandicoot (Perameles bougainville). While initially successful, the unexpected discovery of a papillomatosis and carcinomatosis syndrome in captive and wild populations of P. bougainville exposed a dearth of knowledge regarding their diseases. This dissertation addresses this issue through study of the clinical pathology, immunology, parasitology, and virology of P. bougainville. To facilitate the detection and understanding of diseases in P. bougainville, guidelines for interpreting haematology and clinical chemistry results were developed, including calculated species-specific reference intervals for plasma aspartate transaminase activity (20-283 U/L), haemoglobin (122-165 g/L), haematocrit (0.36-0.49 L/L), total leukocytes (2.9-14.9 x10^9/L), monocytes (0-0.6 x10^9/L), eosinophils (0-0.9 x10^9/L) and total protein (47-63 g/L) estimated by refractometry. P. bougainville immunoglobulin was also fractionated from plasma and inoculated into sheep to derive antiserum for serological screening assays. Arthropods, helminths and protozoa parasitic on P. bougainville were catalogued and Eimeria kanyana n. sp. was formally described. The pathogenic and zoonotic potential of bacteria detected in ticks parasitic on P. bougainville was also considered. The association between bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) and the western barred bandicoot papillomatosis and carcinomatosis syndrome was investigated using PCR, in situ hybridization and virus isolation. Optimized in situ hybridization techniques demonstrated BPCV1 DNA within keratinocyte and sebocyte nuclei, and BPCV1 mRNA within the cytoplasm. BPCV1 virions were isolated by ultracentrifugation and visualized with negative stain transmission electron microscopy revealing icosahedral, non-enveloped viral capsids ~47 nm in diameter, comparable to viruses classified within Papillomaviridae and Polyomaviridae. A novel virus, tentatively named bandicoot papillomatosis carcinomatosis virus type 2 (BPCV2) was discovered in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus). It had a circular double-stranded DNA genome of 7277 bp, and encoded two papillomavirus-like structural proteins, L1 and L2, and two polyomavirus-like putative transforming proteins, large T antigen and small t antigen. DNA and RNA in situ hybridization confirmed the presence of BPCV2 nucleic acids within lesion biopsies. The discovery of the bandicoot papillomatosis carcinomatosis viruses has provoked reassessment of the established virus taxonomy paradigm, theories of virus-host co-speciation and bandicoot population management strategies.

For more than a decade, community groups, scientific organizations and government agencies have collaborated to repopulate the endangered western barred bandicoot (Perameles bougainville). While initially successful, the unexpected discovery of a papillomatosis and carcinomatosis syndrome in captive and wild populations of P. bougainville exposed a dearth of knowledge regarding their diseases. This dissertation addresses this issue through study of the clinical pathology, immunology, parasitology, and virology of P. bougainville. To facilitate the detection and understanding of diseases in P. bougainville, guidelines for interpreting haematology and clinical chemistry results were developed, including calculated species-specific reference intervals for plasma aspartate transaminase activity (20-283 U/L), haemoglobin (122-165 g/L), haematocrit (0.36-0.49 L/L), total leukocytes (2.9-14.9 x10^9/L), monocytes (0-0.6 x10^9/L), eosinophils (0-0.9 x10^9/L) and total protein (47-63 g/L) estimated by refractometry. P. bougainville immunoglobulin was also fractionated from plasma and inoculated into sheep to derive antiserum for serological screening assays. Arthropods, helminths and protozoa parasitic on P. bougainville were catalogued and Eimeria kanyana n. sp. was formally described. The pathogenic and zoonotic potential of bacteria detected in ticks parasitic on P. bougainville was also considered. The association between bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) and the western barred bandicoot papillomatosis and carcinomatosis syndrome was investigated using PCR, in situ hybridization and virus isolation. Optimized in situ hybridization techniques demonstrated BPCV1 DNA within keratinocyte and sebocyte nuclei, and BPCV1 mRNA within the cytoplasm. BPCV1 virions were isolated by ultracentrifugation and visualized with negative stain transmission electron microscopy revealing icosahedral, non-enveloped viral capsids ~47 nm in diameter, comparable to viruses classified within Papillomaviridae and Polyomaviridae. A novel virus, tentatively named bandicoot papillomatosis carcinomatosis virus type 2 (BPCV2) was discovered in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus). It had a circular double-stranded DNA genome of 7277 bp, and encoded two papillomavirus-like structural proteins, L1 and L2, and two polyomavirus-like putative transforming proteins, large T antigen and small t antigen. DNA and RNA in situ hybridization confirmed the presence of BPCV2 nucleic acids within lesion biopsies. The discovery of the bandicoot papillomatosis carcinomatosis viruses has provoked reassessment of the established virus taxonomy paradigm, theories of virus-host co-speciation and bandicoot population management strategies.

Molecular methods have recently revealed novel organisms inhabiting native Australian ticks, some of which are potentially pathogenic due to their similarity to causes of known tick-borne diseases (TBDs) worldwide. Australian bandicoots (Order: Peramelemorphia) are hosts of ticks that are known to bite humans. The persistence of bandicoots in urban and peri-urban areas results in increased exposure of humans to bandicoot ticks, and the bacterial diversity of ticks parasitising bandicoots is therefore of public health interest and requires further investigation. This study analysed 290 ticks parasitising bandicoots from New South Wales (NSW; n = 125), Queensland (QLD; n = 26), Northern Territory (NT; n = 15), Tasmania (TAS; n = 80), and Western Australia (WA; n = 44). A total of seven tick species (Haemaphysalis bancrofti, H. humerosa, Ixodes australiensis, I. fecialis, I. holocyclus, I. myrmecobii and I. tasmani) were identified from four Australian bandicoot species; the eastern barred bandicoot (Perameles gunnii), the long-nosed bandicoot (P. nasuta), the northern brown bandicoot (Isoodon macrourus), and the southern brown bandicoot (I. obesulus). Next Generation Sequencing (NGS) targeting the ubiquitous bacterial 16S rRNA gene was applied to a sub-sample of ticks (n = 66). Analysis of sequence data revealed the presence of Anaplasma, Borrelia, Ehrlichia and ‘Ca. Neoehrlichia’. Anaplasma bovis was detected in two ticks (H. bancrofti and H. humerosa) from the same bandicoot in NSW. A likely novel Ehrlichia sp. was identified from a single I. fecialis tick in WA. In addition to the confirmation of the recently described ‘Ca. Neoehrlichia arcana’ and ‘Ca. N. australis’ inhabiting I. holocyclus and I. tasmani from NSW and QLD, a novel ‘Ca. Neoehrlichia’ species was detected in ticks (I. australiensis and I. fecialis) from WA. Furthermore, sequences 98.8% similar to ‘Ca. Borrelia tachyglossi’ provide the first molecular description of Borrelia inhabiting ticks (H. humerosa and I. tasmani) parasitising Australian bandicoots. This study has provided an interesting insight into the microbial communities present in ticks parasitising Australian bandicoots and raises questions about the potential for tick-associated illness in people parasitised by these ticks. An investigation into the characterisation, prevalence, pathogenicity and transmission dynamics of these candidate tick-borne pathogens is required to establish the significance of this study.

Evolution through natural selection enables species to adapt to their surroundings and optimise themselves for reproduction and survival. Sexual selection, on the other hand, reflects modifications to improve reproductive fitness of individuals within species. Animal morphology, therefore, often represents a compromise between these two selective pressures. Bandicoots and bilbies (Marsupialia; Peramelemorphia) are small to medium sized omnivorous marsupials, of which roughly 30 species inhabit varied habitats throughout Australia and Papua New Guinea. This study sought to quantify craniodental variation in a range of bandicoot and bilby species to investigate the relationship between natural selection and sexual dimorphism in this clade of animals. Micro-CT and laser scanning techniques were employed to obtain three-dimensional scans of the crania and dentition of the 25 study species and subspecies (total n=124; 63 female and 61 male). Landmark analysis was conducted on 54 landmarks placed on the cranium and upper dentition to pinpoint areas of variation within and between the genera, species and sexes. Interspecific variation in cranial morphology between genera and species does reflect taxonomic groups and likely reflects adaptation by natural selection for different ecologies in different clades. Macrotis was the closest to the consensus shape for Peramelemorphia. Within family Peramelidae, genera formed discrete clusters, reflecting diagnostic differences in cranial shape between the two genera, separating Australian the short-nosed bandicoots (Isoodon) from the long-nosed or barred bandicoots (Perameles). The Peroryctidae clustered together, with Peroryctes nested within Echymipera, and Microperoryctes between Echymipera and Macrotis. Echymipera kalubu was the only exception and nested within Macrotis, quite distinct from the other species of Echymipera. Intraspecific variation showed strong evidence of sexual dimorphism in the species Macrotis lagotis and Isoodon fusciventer, while most other species did not have sexual dimorphism. In the two species that did show dimorphism in skull shape, there is also significant dimorphism in body mass, with males typically being larger. Shape changes did have allometric correlations with skull size, in PC axis 1 in M. lagotis and interestingly in PC axis 2 in I. fusciventer. In P. papillon, one of the smallest species, there was a trend towards female biased sexual dimorphism both size and skull shape, though this was not significant in our sample. This study highlights the large range of expressions of craniodental sexual dimorphism present in Peramelemorphia, and quantifies distinctions between expression within and between genera.

Hearing is an important factor allowing species to obtain information about their environment. Variation in tympanic bullae and external pinnae morphology has been linked with hearing sensitivity and sound localisation in different mammals. Bandicoots and bilbies (Order Peramelemorphia) typically occupy omnivorous niches across a range of habitats from open, arid deserts to dense, tropical forests in Australia and New Guinea. The morphology of tympanic bullae and pinnae varies between peramelemorphian taxa. Little is known about the relationship between these structures, or the extent to which they vary with respect to aspects of ecology, environment or behaviour. This thesis investigated the relationship between tympanic bulla and pinna size in 29 species of bandicoot and bilby. Measurements were taken from museum specimens to investigate this relationship using direct measuring methods and linear dimensions. It was hypothesised that an inverse relationship between bullae and pinnae may exist and that species residing in arid regions would have more extreme differences. Environmental variables were examined to determine the level of influence they had on bullae and pinnae. This study found that there was a phylogenetic correlation between the structures and that they were significantly influenced by temperature (max/average) and precipitation (average). Species which inhabited more complex, temperate habitats had relatively smaller bullae and pinnae than those in less complex, more arid habitats. Species tended to have either a relatively larger bulla or pinna, with the relationship being more pronounced in species in more arid habitats. No inverse relationship was found between relative bulla and pinna size. Previous studies have found a relationship between relative bulla and pinna and predator evasion tactics; the findings of this study appeared to support this. These findings suggest that ecological traits and habitat types may be linked with relative bullae and pinnae sizes.

Odour plays an important role in many predator/prey interactions. In the northern hemisphere, many mammalian prey species have been shown to respond to predator odours. It is also widely assumed that mammalian predators utilise odours to locate their prey. This thesis explores the importance of odour in Australian mammalian predator/prey interactions. Responses of native Australian species to the faecal odour of two predators; the native tiger quoll Dasyurus maculatus and the introduced red fox Vulpes vulpes, were evaluated through live-trapping and focussed behavioural studies of captive animals. Tiger quoll responses to prey olfactory cues were investigated in a captive experiment. Native rodents (bush rats Rattus fuscipes, swamp rats R. lutreolus and eastern chestnut mice Pseudomys gracilicaudatus) equally avoided traps scented with either quoll or fox faeces, and in captive experiments, bush rats and swamp rats reduced their average speed in response to both predator odours. Of the marsupial species, northern brown bandicoots Isoodon macrourus and common brushtail possums Trichosurus vulpecula were captured more frequently in quoll-scented traps than unscented traps or foxscented traps, while captures of brown antechinus Antechinus stuarttii, long-nosed bandicoots Perameles nasuta and southern brown bandicoot I. obesulus were unaffected by the either predator odour. In captive experiments, brown antechinus, long-nosed and northern brown bandicoots decreased their foraging in response to both predator odours, and spent less time in areas scented with quoll faeces. Tiger quolls didn't appear to detect odour sources from a distance of >65 cm, but they did follow scent trails and spent more time in areas scented with the urine and faeces of potential prey. Chemical analysis revealed no common components in fox and quoll odour which prey species could be responding to. Therefore, these native species have evolved to respond to fox odour since foxes were introduced to Australia 130 years ago. The stronger response of native rodents to fox odour may be a legacy of their co-evolution with canid predators prior to entering Australia. A better understanding of how odour is utilised in Australian predator/prey interactions may lead to a greater ability to protect Australia's unique mammalian fauna from introduced predators.

Longtemps considérés en Thaïlande comme simple gibier mais souvent destructeurs des cultures, les rats et les souris (Murinae) se sont révélés d'importants vecteurs de germes pathogènes pour l'Homme, depuis l'émergence soudaine de la leptospirose en 1996. Ils sont aussi responsables de la transmission du typhus des broussailles et probablement d'hantaviroses dont l'incidence reste suspectée. Cette thèse a pour objectif d'analyser la géographie de ces zoonoses afin d'en mesurer le risque de transmission à l'Homme.
Un important travail de terrain a permis de collecter et d'étudier les rongeurs murins dans différents milieux représentatifs de leur diversité. Parallèlement, une enquête conduite dans la province de Phrae a montré la variabilité du système de soins et des comportements de santé. Un Système d'Information Géographique « Rongeurs et santé » centralise l'intégralité des données sur l'ensemble du territoire pour une analyse spatio-temporelle.
Cette recherche a permis de mettre à jour la description et la distribution par télédétection des principaux rongeurs murins thaïlandais ainsi que leur implication dans la transmission de germes pathogènes. La géographie de ces zoonoses reflète des différences de niveau de vie : l'exposition de l'Homme à ces maladies résulte de la chasse et de la consommation de rongeurs mais aussi d'un accès et d'un recours aux soins limités, traduisant ainsi la pauvreté des populations touchées.
Ce travail offre une approche critique des méthodes alliant les outils de la géomatique, l'analyse spatiale et la télédétection, pour l'étude des zoonoses.

碩士
東海大學
生命科學系
97
Abstract Bandicota indica is the largest muridae animal distributed in Southeast Asia, and also the biggest rodent generally habitat at lower elevation area in Taiwan. Swinhoe (1870) speculated that this rat had been introduced to Taiwan by the Dutch in the 17th century, but lacking the historical evidence. From the view of the genetics, species colonize a new environment should affect by the founder effect or the bottleneck effect, exhibiting a lower genetic diversity. The evolutionary history of the species could be traced by understand the genetic variations, population divergence and phylogenetic relationships of the populations in different geographical regions. In this study, I used the d-loop region and cytochrome b gene sequences of the mitochondrial DNA to reconstruct the phylogenetic trees in order to understand the population genetic structure of Bandicota indica in Taiwan, and examine the phylogenetic relationships of samples from Fujian, Guangdong, and Vietnam. I used the haplotypes network and mismatch distribution analysis to examine any genetic pattern of the recent introduced species in Bandicota indica. The phylogenetic analysis of the d-loop partial sequence (700 base pairs) and cytochrome b gene complete sequence (1140 base pairs) can separate the Taiwan samples into two groups, Taiwan type and Hualien type. The genetic distance and sequence divergence were high between two types. Most of the variance is between two types in AMOVA analysis and the gene flow was low. The large divergent star-like structure in cytochrome b gene haplotypes network of Taiwan types was not consist with the pattern of recent introduced species. The unimodal displays in mismatch distribution analysis revealed the population expansion of Taiwan types, and closely relationships between Taiwan types and Fujian haplotypes suggest that the rat might have been colonized from mainland. The high genetic diversity of cytochrome b sequences in Hualien types might be resulted from the multiple introduction events. In this study, however, I excluded the Fujian, Guangdong, and Southern Vietnam as the possible origin of the Hualien types. Futher investigation on relationships among populations of Hualien and Northern Vietnam and other regions of Southeast Asia should be conducted in detail with more samples.

In this study, the changes of the milk components (protein, carbohydrate, lipids and total solids) were investigated during part of the lactation period of the P. gunnii (4 to 8 weeks) and compared with other marsupial species and with Wombaroo® milk formula. It was found that protein increased during early, mid and late stage of lactation (4.5, 10.2, 12units) lipid (3.1, 8.4, 17.4units) and total solids (28, 36, 54units!), while carbohydrate although increased by the mid stage of lactation (from 2 to 5.5 g 100 m1: 1 ) by the end of lactation dropped to almost initial levels (2.5 g 100 m1: 1 ). The highest value of the energy contents reached 8.86 ± 1.037 KJ mL-1at the end of lactation. The pattern of growth of the pouch young was observed and the changes of the metabolic rate at two different ambient temperatures (25 and 35°C). The onset of endothermy occurred at 7 weeks while at 8 weeks the metabolic rate increased but by 9 weeks had dropped to almost adult levels (0.58 mL g -1h-1 ). The body mass of the young bandicoot increased sigmoidally from 14.84 ± 1.49 g (4weeks) to 120.54 ± 9.67 g (8 weeks), the head length from 31.82 ± 1.36 mm to 60.81 ± 2.16 mm, the tail from 17.4 ± 1.37 mm to 51.45 ± 3.34 mm and the foot length from 18.05 ± 1.82 mm to 53.2 ± 0.8 mm respectively. The fur of P.gunnii was first seen at the age of 6 weeks, while at 8 weeks it was well developed. Measurements of the metabolic rate and of the thermal conductance (TC) of adult P. gunnii were measured at different ambient temperatures. We observed that the thermoneutral zone (TNZ) of the P. gunnii lay between 25 and 30°C. The change in metabolic rate before and after warm (25°C) and cold acclimation (5°C) was observed. Cold acclimated animals increased their metabolic rate, while warm acclimatised animals decreased significantly their metabolic rate (P = 0.03). Norepinephrine (NE) had a significant affect before and after cold acclimation at 25 and 5°C and before (P = 0.03), but not after warm acclimation (P = 0.06). Additionally, electromyography (EMG) measurements showed a reduction of shivering after cold acclimation (P = 0.04). NE had a significant affect on what! before (P = 0.003) but not after cold acclimation (P = 0.08). On the other hand NE did not reduce significantly shivering at 25°C before or after cold acclimation (P = 0.22, P = 0.25).

The reasons for the population decline of the marsupial the Eastern Barred Bandicoot, Perameles gunnii, in Tasmania, and the probable role of their susceptibility to protozoan diseases such as Toxoplasma gondii remain elusive. The pathological hallmarks of the disease have been extensively investigated in other animal species and although some species are more vulnerable to toxoplasmosis than others, the reason for marsupial vulnerability remains to be fully defined. This thesis has sought to address these and other factors that might be associated with the relationship between the marsupial, its microbial and parasitic diseases, ecological surroundings and immune system. Secondly, it was essential to examine the current disease status of P. gunnii in relation to its zoonotic potential in the Tasmanian setting. Finally, it was necessary to attempt to investigate the immunological status of this animal. The major conclusions from these investigations were that P. gunnii is extremely susceptible to even low doses of T. gondii oocysts. The development of clinical disease is rapid, with high morbidity and mortality. The species appears to be susceptible to other Apicomplexan species including Hepatozoon sp., and the flagellate Giardia. The close association of P. gunnii with humans and the infringement of humans into their habitat makes this marsupial vulnerable to trauma, predation, shelter and food deprivation, and exacerbation of current parasitic and microbial diseases. In summary, this study further clarifies the relationship between humans, P. gunnii and parasite and the possible zoonotic potential that exists within Tasmania.

Habitat loss and fragmentation are major threats to the world’s biodiversity. Throughout Australia, land has been extensively cleared and modified through agriculture, forestry and urbanisation. In South Australia, less than 20% of native forests and woodlands remain and many of these have been severely fragmented into smaller and isolated patches. Species inhabiting fragmented habitats can suffer from decreased population size, reduced or inhibited dispersal and a series of genetic risks, including inbreeding, reduced genetic diversity, increased genetic differentiation among populations and potentially increased extinction risk. The southern brown bandicoot (Isoodon obesulus), the focus of the current thesis, is a rabbit-sized ground-dwelling marsupial, which has declined in number dramatically over the last 220 years. The subspecies I. o. obesulus is listed as nationally endangered under the Australian Environment Protection and Biodiversity Conservation Act 1999. Habitat loss and fragmentation has become one of the main processes threatening the survival of I. obesulus, leading to a contracted distribution and local population extinctions throughout Australia. In this thesis, a combination of microsatellite, nuclear and mitochondrial markers have been applied to investigate several questions relating to population genetic structure, gene flow, dispersal and genetic distinctiveness of populations of I. o. obesulus in southern Australia. The results obtained in this thesis have increased our knowledge of the genetic connectivity of I. o. obesulus populations in fragmented landscapes and provided valuable baseline genetic information for the conservation management of the species. This thesis was structured into four distinct data chapters as explained below. Chapter Two comprises a published primer note, in which nine polymorphic microsatellite markers were developed using a next generation sequencing approach. The markers were genotyped in 59 individuals from two distinct locations (the Mount Burr Range and the Mount Lofty Ranges) in South Australia. These markers, in addition to six microsatellite markers from a previous study, were used for the following thesis chapters and provide a valuable resource for future molecular ecological studies of I. obesulus. In Chapter Three, I investigate population structure and gene flow/dispersal of I. o. obesulus within a fragmented forest system in south-east South Australia – the Mount Burr Range. In this fragmented habitat, native forest patches are surrounded by matrices of either Pinus radiate plantations or cleared agricultural land. A total of 147 samples from 14 native forest patches were genotyped at 15 microsatellite loci. The results showed significant population genetic structuring at a fine spatial scale, with strong genetic differentiation among patches. Gene flow and dispersal was limited and generally only among neighbouring patches. The findings contribute valuable information on the positioning of habitat corridors in this area, and enable the effectiveness of these corridors to be assessed in the future. In the fourth chapter I utilise 14 microsatellite markers to genotype 284 individuals from 15 sites in a heavily modified peri-urban landscape in South Australia – the Mount Lofty Ranges. The results showed significant genetic differentiation among sites. Sites in the central Mount Lofty Ranges were also more genetically differentiated than sites distributed over a similar spatial scale in the Mount Burr Range, with evidence for a dispersal threshold of 1km (the Mount Burr populations had a ~2.5 km dispersal threshold), and with two sites appearing to be genetically isolated. These analyses suggested that gene flow/dispersal was limited to a higher degree in the Mount Lofty Ranges compared to Mount Burr, possibly due to the heavily modified landscape in the former area (e.g. a mixture of matrix of urban constructs and agricultural land). The final data chapter (Chapter Five) investigates the phylogeography and population structure of the I. o. obesulus populations in South Australia and south-western Victoria using a combination of 14 microsatellite markers, two mitochondrial sequence markers (control region and ND2) and three nuclear sequence markers (BRCA1, RAG1, and vWF). This chapter aimed to identify any potential evolutionarily significant units (ESUs) in the study region. All markers supported two distinct genetic lineages of I. o. obesulus in South Australia and south-western Victoria. The first lineage consisted of individuals from the Mount Lofty Ranges and Kangaroo Island. Samples from the lower south-east of South Australia and south-western Victoria (the Grampians and Lower Glenelg) represented the second lineage. These two lineages should be considered as separate evolutionarily significant units and managed separately for conservation purposes. An expanded phylogenetic analysis was conducted using additional samples of I. obesulus from other regions in Australia and samples of I. auratus (the golden bandicoot, distributed in the Northern Territory and Western Australia). The results raise the issue of the taxonomic status of the two lineages and also suggest that current subspecies and species classification within I. obesulus/I. auratus may not adequately reflect the existing major genetic lineages.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2014

Management of fire and fire regimes is an important part of reserve management. In Australia, fire is used as a management tool to protect human infrastructure and cultural and natural assets. It is also used in reserve management to reduce fuel loads and promote the regrowth of fire-dependent vegetation. Many vertebrate species depend upon the naturally occurring spatial mosaic of burnt and unburnt vegetation for survival with some taxa being associated with frequent fires while others are fire-sensitive and cannot tolerate frequent disturbances such as fires. In this thesis, I present the results of a long-term study of the terrestrial marsupial the Long-nosed Bandicoot (Perameles nasuta) in a highly heterogeneous and fire-prone landscape. I studied the species at Booderee National Park where there was a major wildfire in 2003 and other smaller wildfires since that time. Understanding how animals use heterogeneous environments and how disturbances such as fire influence habitat use is vital for wildlife management. I found that the Long-nosed Bandicoot showed a preference for particular types of vegetation in which to forage, especially unburnt vegetation. While fire did not significantly alter home-range size, it did influence the way animals used their home range. It is also important for wildlife management to determine the spatial and temporal pattern of refugia used within a heterogeneous landscape affected by fire. Sixty per cent of nests of the Long-nosed Bandicoot within the footprint of burnt forest and woodland habitat were in unburnt patches. These nests were significantly larger and were used more frequently than nests located in burnt microhabitat. Within areas broadly subject to fire, the Long-nosed Bandicoot typically constructed nests located in unburnt areas with dense grasses and a dense midstorey. However, the species also nested in open areas and responded to fire-affected areas by constructing smaller nests. It is also important to consider temporal and spatial scales in the management of biodiversity. In the short term, the wildfire affected how individual Long-nosed Bandicoots associated with their immediate habitat but in the longer term, it had limited effect on where they occurred in the broader landscape. I found that the spatial occurrence of the Long-nosed Bandicoot at Booderee National Park was more likely to be influenced by the relative amount of leaf litter than it was by the 2003 wildfire.

An investigation was undertaken into the diet and comparative feeding ecology of the Tasmanian Bandicoots, Perameles gunnii and Isoodon obesutus affinis. Studies on captive specimens revealed that both P. gunnii and I. obesutus detected significantly more cups containing ground cockroach extract than non-extract cups buried at various depths. However, only P. gunnii located significantly more cups containing earthworm extract than non-extract cups. Auditory trials demonstrated that P. gunnii and I. obesutus do not appear to depend on hearing to locate prey. Olfaction appears to be the primary prey detection strategy employed by bandicoots. Digestibility trials revealed that soft-bodied prey such as earthworms may be totally digested, hence they appear absent in bandicoot faeces. Soft-bodied insects e.g. cockroaches, although identifiable in faeces, are difficult to quantify due to the digestive fragmentation of potentially quantifiable structures. From their diet in southern Tasmania, P.gunnii and I. obesutus appear to be qualitatively opportunistic omnivores, feeding on a wide range of prey available, but apparently not always in proportion to which they occur. The overlap in 36 prey categories is positively correlated for each of the Peramelids with only two taxa showing significant differences in the total diets between the two species. Significantly more I. obesutus scats than P. gunnii samples were collected containing bees and wasps (Hymenoptera); significantly more P. gunnii faeces were obtained containing Clover (Trifolium repens). The diet would largely appear to reflect seasonally and locally abundant food items. The most important dietary items for I. obesutus in autumn appeared to be ants (Formicidae), maggots (Calliphoridae larvae), Rove beetles (Staphylinidae), mature Coleopterans, Scarabaeidae larvae, Hymenopterans and Hemipterans, while those of P. gunnii were larvae, spiders (Araneae), flies (mature Diptera), Calliphoridae larvae, ants, ground beetles (Carabidae) and their larvae. Blackberries, Monocot and a Zygomycete fungus were important plant components in faecal pellets of both species, and Moss and nodules in P. gunnii. Two faecal pellets in winter for P.· gunnii revealed Scarabaeidae larvae, Calliphoridae larvae, armyworms (Noctuidae), Springtails (Collembola) in half of the sample while Clover root nodules and seeds occurred in both scats. In I. obesulus, Scarabaeidae larvae, ants, Carabidae larvae, mature Coleoptera, seeds, Monocot, nodules and Gasteromycete fungus occurred in more faecal pellets for the winter session than other prey taxa. In spring, a marked increase in E/S/C larvae correlated with an increase in this category in the faeces of both bandicoot species. Corbie grubs (Hepialidae), spiders, Rove beetles, Monocot, seeds and Clover root nodules occurred in more scats of I. obesu'lus, relative to other taxa. For P; gunnii, armyworms appeared to be most important with larvae, Mites (Acarina), Scarabaeidae larvae, mature Coleoptera, Monocot, seeds and roots. Slight diet differences were observed between habitats for I. obesulus and appeared to reflect the local availability of prey items. Prey size selection indicated that I.obesulus and P; gunnii appear to take a similar size of prey (approximately 11-11.5 mm); however the number of samples recorded for P; gunnii was small: No correlation appeared to exist between predator weight (I. obesulus) and mean prey size as determined by regression equations relating insect tarsal widths from faeces to those of insects of a known length. Bimodal capture-success-curves were recorded for I. obesulus possibly due to the inclusion of elongate Rove beetles and small prey (1-2 and 2-3 1 in winter) when larger prey appeared to decrease in availability. However, I; obesulus predominantly selected larger size classes of prey than those available. Diet does not seem to be a significant factor in the apparent spatial, ecological separation exhibited by the two Peramelid species. Temporal segregation may be additionally important in reducing competition between I. obesulus and P. gunnii.