Dissertations / Theses on the topic 'Australian mammals'

The aim of this project was to study the nature and relative proportion of the volatile components in the sternal-gland secretions obtained from a wide range of Australian marsupials.The results obtained were then used to investigate the evolution of semiochemicals in Australian marsupials by using the current phylogenetic tree as a template.The initial part of the study was dedicated to the investigation of some of the techniques available for the sampling and analysis of gland secretions. Individuals from 8 families within the Marsupialia and 1 family from the Monotremata were sampled over an 18 month period.The obtained results were then subjected to multivariate statistical analysis followed by cladistic analysis.In several species the secretion composition was found to be affected by the breeding status of individuals for both genders.Many other factors such as animal-age, hierarchical status, diet,and lifestyle were also observed to affect the secretion composition. Finally, cladistic analysis demonstrated the differences in the levels of divergence at the species, familial and ordinal levels and highlighted secretion components that could be used to differentiate between super families, species and even sexual status of individuals.
Master of Science (Hons)

This thesis began as an investigation into evolution of the platypus family (Ornithorhynchidae, Monotremata), now known from both Australia and South America. The thesis broadened its scope with inclusion of non-ornithorhynchid Mesozoic monotremes from Lightning Ridge, NSW. This change in direction brought an unexpected result: a fossil mammal from Lightning Ridge investigated for this thesis (presumed to be monotreme: Flannery et al., 1995) appears to be a new and unique type of mammal. Specimens were procured through Queensland Museum (Riversleigh material); Australian Museum (Lightning Ridge material); and Museum of Victoria and the South Australian Museum (fossil ornithorhynchids). Specimens were examined under a light microscope and scanning electron microscope; specimens were photographed using light photography and a scanning electron microscope; and illustrations and reconstructions were done with a camera lucida microscope attachment and photographic references. Parsimony analysis utilised the computer programs PAUP and MacClade. Major conclusions: 1) analysis and reconstruction of the skull of the Miocene platypus Obdurodon dicksoni suggest this robust, large-billed platypus was a derived northern offshoot off the main line of ornithorhynchid evolution; 2) the well-preserved skull of Obdurodon dicksoni shows aspects of soft anatomy previously unknown for fossil ornithorhynchids; 3) two upper molars from Mammalon Hill (Etadunna Formation, late Oligocene, central Australia) represent a third species of Obdurodon; 4) the South American ornithorhynchid Monotrematum sudamericanum from the Paleocene of Argentina is very close in form to the Oligocene-Miocene Obdurodon species from Australia and should be considered congeneric; 5) a revised diagnosis of the lower jaw of the Early Cretaceous monotreme Steropodon galmani includes the presence of two previously undescribed archaic features: the probable presence of postdentary bones and a meckelian groove; 6) morphological evidence is presented supporting a separate family Steropodontidae; and 7) analysis of new fossil material for Kollikodon ritchiei suggests that this taxon is not a monotreme mammal as originally identified but is a basal mammal with close relationships to allotherian mammals (Morganucodonta; Haramiyida). Kollikodon is provisionally placed as basal allotherian mammal (Allotheria sensu Butler 2000) and is unique at the ordinal level, being neither haramiyid nor multituberculate. A new allotherian order ??? Kollikodonta ??? is proposed.

The aim of this project was to study the nature and relative proportion of the volatile components in the sternal-gland secretions obtained from a wide range of Australian marsupials.The results obtained were then used to investigate the evolution of semiochemicals in Australian marsupials by using the current phylogenetic tree as a template.The initial part of the study was dedicated to the investigation of some of the techniques available for the sampling and analysis of gland secretions. Individuals from 8 families within the Marsupialia and 1 family from the Monotremata were sampled over an 18 month period.The obtained results were then subjected to multivariate statistical analysis followed by cladistic analysis.In several species the secretion composition was found to be affected by the breeding status of individuals for both genders.Many other factors such as animal-age, hierarchical status, diet,and lifestyle were also observed to affect the secretion composition. Finally, cladistic analysis demonstrated the differences in the levels of divergence at the species, familial and ordinal levels and highlighted secretion components that could be used to differentiate between super families, species and even sexual status of individuals.

Australian mammals have fared badly over the past 200 years with 17 species extinct, 10 species surviving only on islands, and another 17 reduced to remnant populations of less than 10% of their range at the time of European settlement. Most extinct or threatened species fall within a critical weight range of 35 g to 5,500 g (CWR), as defined by Burbidge and McKenzie (1989). A disproportionate number come from arid and semi-arid Australia. This thesis poses the questions: Why have these species proved so vulnerable and what can be done to redress the situation? Section 2 describes a particular CWR species - the Burrowing Bettong Bettongia lesueur. The Burrowing Bettong is a small macropod that is extinct on the Australian mainland, but survives as remnant populations on offshore islands. Study of this species has been largely neglected due to the relative isolation of its surviving populations and the belief that they may be secure because of that isolation. I surveyed four islands on which Burrowing Bettongs occurred to establish their abundance and distribution; to assess the major factors impacting on their abundance; and to detail their ecology. Section 3 briefly summarises the controversy surrounding the loss of CWR mammals. Is the primary cause of their decline and extinction due to a decline in habitat and habitat quality, to predation, or to some other factor or combination of factors? Previous major reviews have been comprehensive and inclusive, generally concluding that declines and extinctions of fauna are due to complex interactions of many factors. While the value of such reviews is acknowledged, my approach has been more pragmatic. I approached the issues from the view of a manager whose primary aim is an on-ground result: successful re-establishment of populations of threatened species after an absence of more than half a century. I took a hierarchical view of threatening processes seeking to identify and focus on the process most likely to limit successful reintroduction. Section 3 includes three discrete bodies of research that each probe the cause or causes of mammal decline. The first examines the distribution, abundance and ecology of CWR mammals (including the Burrowing Bettong) on Barrow Island as influenced by vegetation mosaic. The second examines the historical record of bounty payments made on rat-kangaroos in New South Wales (the Burrowing Bettong is one of five species) to establish the spatial and temporal pattern of decline. This decline is juxtaposed against the major ecological events of the time: Sheep, Rabbits, Foxes and drought. The third collates and synthesises unpublished data on twenty five past reintroductions of macropods in an attempt to identify threatening processes and threatening practices. One such attempt was the unsuccessful introduction of Burrowing Bettong to Kangaroo Island in South Australia in the 1920s. Section 4 details the reintroduction of the Burrowing Bettong from Dorre Island to Heirisson Prong at Shark Bay. This was the first reintroduction of this species to mainland Australia and was conducted against a background of past failure or limited success of reintroductions to arid and semi-arid Australia. This study pioneered or advanced a number of innovative techniques: the use of peninsulas to gain advantages in predator control; the use of a number of complementary barriers of defence against predators to minimise incursions, and in situ captive breeding of the endangered species in its natural habitat to provide a pool of animals for release over successive years (a buffer against demographic and environmental stochasticity and providing for adaptive development of predator control methods). The reintroduced population of Burrowing Bettongs on Heirisson Prong represents the first mainland population for over 50 years. An initial group of twelve animals were transferred from Dorre Island in May 1992 and a first release to the wild was made in September 1993. The population has persisted in the wild for over five years and now exceeds 130 animals and is continuing to grow. Its continued survival depends on ongoing predator control. Section 5 reviews the historical pattern of decline of mammals and the range of threatening processes that might be responsible. There appear to have been at least two major periods experiencing high loss of mammals in post-European times. The mainland extinction of the Burrowing Bettong forms part of the second phase - attributed primarily to predation by Foxes. The first period of loss coincided with, or immediately post-dated, European pastoral expansion. Typically, species lost during this period were smaller species within the CWR (< 350 g). These species may have been unable to cope with habitat alteration caused by stocking; or they may have been victims of the colonisation of the continent by another exotic predator - the feral Cat. The early loss of smaller species on both sides of the continent suggests the latter. Suggestions in the literature that Cats became established across Australia in pre- European times suggest otherwise. However, I provide some evidence to suggest Cats may have become established in the early pastoral phase of post-European Australia. Hence, predation by Cats provides a plausible explanation for the early loss of mammals. The research within this thesis is firmly embedded in the “declining population paradigm” of Caughley (1994) and has made little or no use of the new tools of the “small population paradigm”. I have assumed that the cause of declines and extinctions is some external agent and I have sought to identify that agent and ameliorate its impact. Caughley’s criticism of the “declining population paradigm” is that it represents a case-by-case zoological investigation to solve problems of particular species threatened with extinction. This does not appear to be true in this instance. The CWR mammals appear to have suffered broadly similar fates. Hence solutions generated for one species should have broad application to a suite of species. The conclusions may also generalise to extinctions and declines at many other insular situations that have been invaded by humans and their pest species in historic times. The body of research within this thesis has advanced the general understanding of the processes of extinction of CWR mammals and provided the knowledge to successfully re-establish at least one species to the mainland from remaining relict populations on off-shore islands. It has led, also, to further related work on the control of predators; the behaviour of native species that make them vulnerable to predation by exotic predators; the behaviour of predators that led to a scale of impact greater than one might expect from predator-prey theory; and provides baseline data for modeling the interaction between predator and prey.

Blood-borne and enteric protozoan parasites belonging to the genera Trypanosoma, Babesia, Theileria, Cryptosporidium and Giardia are responsible for severe animal and human illnesses worldwide. In addition, parasites of the genus Hepatozoon have been associated with animal morbidity and mortality. Despite recent research and improved knowledge of the taxonomy and distribution of native Australian protozoan parasites, still relatively little is known about their epidemiology, genetic diversity and pathogenicity. The overarching aim of this thesis was to determine the prevalence, molecular characterisation and potential clinical impact of protozoan pathogens of potential conservation and zoonotic importance in Australian native mammals. A total of 465 blood samples, 167 faecal samples and 91 ticks were collected from mammals belonging to seven target species: common brush-tailed possums (Trichosurus vulpecula), northern brown bandicoots (Isoodon macrourus), northern quolls (Dasyurus hallucatus), brush-tailed rabbit-rats (Conilurus penicillatus), koalas, a little red flying fox (Pteropus scapulatus) and grey-headed flying foxes (Pteropus poliocephalus). The sampling was undertaken across four states/territories in Australia: the Northern Territory (NT), Queensland (Qld), New South Wales (NSW) and South Australia (SA). Molecular and morphological analyses were utilised to identify and characterise Trypanosoma, Babesia, Theileria, Hepatozoon, Cryptosporidium and Giardia. The potential clinical impact of the parasites identified was investigated by associating clinical, haematological and biochemical parameters, whenever available, with presence or absence of infection. A molecular survey was conducted in the NT to investigate the prevalence, genetic diversity and potential pathogenicity of protozoan parasites in common brush-tailed possums, northern brown bandicoots, northern quolls, and brush-tailed rabbit-rats. Overall, 22.5% (95% confidence interval (CI): 17.0-28.8%) of the animals tested were positive for haemoprotozoans by Polymerase Chain Reaction (PCR) targeting the 18S ribosomal RNA (rRNA) gene. Trypanosoma vegrandis and T. noyesi were found in 26.6% (95% CI: 18.7-35.7%) of the bandicoots and in 23.7% (95% CI: 11.4-40.2%) of the possums, respectively. Babesia spp. and Hepatozoon spp. were identified in bandicoots only, both at a prevalence of 5.3% (95% CI: 2.7-9.3%). Hepatozoon gamonts were detected using light microscopy in two out of 11 animals positive for this parasite by PCR. Faecal samples were tested for Cryptosporidium spp. at the 18S rRNA locus, and for Giardia spp. at the glutamate dehydrogenase (gdh) and 18S rRNA loci. The total prevalence of intestinal protozoan parasites observed was relatively low (3%; 95% CI: 1.0-6.9%). No clear signs of major morbidity were observed in infected animals, however bandicoots positive for Trypanosoma exhibited a significantly lower packed cell volume (PCV) compared to negative bandicoots (p = 0.046). The first report of T. vegrandis in koalas using morphology and sequence analysis of the 18S rRNA gene is also described. The prevalence of T. vegrandis in koalas was (13.6%; 95% CI: 5.2-27.4%). In addition, a novel next-generation sequencing (NGS)-based assay for Trypanosoma, developed during the present study, revealed that mixed infections with up to five trypanosome species in koalas were significantly more prevalent (27.4%; 95% CI: 21-35%) than single trypanosome infections (4.8%; 95% CI: 2-9%). Infections with T. gilletti, T. irwini, T. copemani and T. vegrandis were identified. Additionally, T. noyesi was detected for the first time in koalas, although at a low prevalence (0.6%; 95% CI: 0-3.3%), and a novel species (Trypanosoma sp. AB- 2017) was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood were identified as T. irwini, suggesting this was the dominant species. The study also employed the NGS methodology to profile trypanosome communities within Ixodes holocyclus and I. tasmani ticks removed from koala hosts. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB- 2017 were also detected in the ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. This thesis also characterised a novel trypanosome species in a little red flying fox with clinical signs of trypanosomiasis, using morphology and molecular analyses at the 18S rRNA and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) loci. Morphological comparison showed that trypomastigotes of the novel species were significantly different from those of Trypanosoma pteropi and T. hipposideri, two species previously described from Australian bats for which genetic information was unfortunately not available. Phylogenetic analysis revealed that the novel species was genetically distinct and clustered with other bat-derived trypanosome species within the Trypanosoma cruzi clade. The discovery of a new bat-derived trypanosome species in Australia prompted the screening of an additional 87 blood samples from grey-headed flying foxes, which were negative for Trypanosoma 18S rDNA. In summary, this research provides new insights on the prevalence, spatial distribution, inter- and intra-specific genetic diversity and the potential negative effects of bloodborne and enteric protozoan parasites on the health of Australian mammals. Furthermore, the identification of trypanosome polyparasitism in koalas and two species of native ticks will inform future epidemiological conservation studies. The outcomes of this thesis may be used to inform wildlife management and zoonotic disease programs.

Cat ownership in Australia is declining compared to an increasing trend of cat ownership in the United Kingdom, United States and Europe. The decline in Australia may be linked to concerns over perceived impacts of cat predation and an associated dislike of cats. However, while there are numerous studies on feral cats and their impacts on declining native fauna, the impact of pet cats on suburban wildlife or fauna in remnant bushland is relatively unknown although there is a wide perception of risk. The primary aim of this thesis was to apply the precautionary principle to the question of the putative impact of pet cats on the abundance and diversity of small mammals in urban bushland adjacent to low-density suburbia in the City of Armadale, a municipality on the south-east fringe of Perth, Western Australia. At the time of writing, Western Australia is yet to introduce state legislation governing cat control although many local councils within the state have either implemented or are in the process of implementing cat regulations. The precautionary principle was deemed an ideal approach to this question, because it provides a rationale for deciding on possible actions where both the potential risk to environmental values and the uncertainty about possible impacts are high. In such cases the precautionary principle requires two broad lines of action: firstly, detailed consultation with stakeholders to determine their perceptions of risk and the actions they are prepared to take to reduce it and, secondly, research to reduce uncertainty. With regard to stakeholder consultation, local residents were surveyed in regard to their attitudes and current cat husbandry practices. A substantial proportion of respondents within this municipality believed cat regulations were necessary (75% of owners and 95% of non-owners). At least 70% of both owners and non-owners agreed with the propositions that cats not owned by licensed breeders should be desexed, local councils should restrict the maximum number of cats that can be owned on one property and that pet cats entering nature reserves are harmful to wildlife. Most (c.85%) cat owners agreed that they would license their cats if that became compulsory. Although fewer owners (c.60%) were prepared to keep their cats on their property at all times to protect wildlife, over 80% were willing to confine their cats at night if it was required. Owners seemed to be substantially motivated by the value of these measures in reducing injury to cats and facilitating the return of lost animals rather than concern over wildlife protection. Attempts to reduce uncertainty involved (i) assessing roaming patterns of pet cats to determine the sizes of appropriate buffer zones around nature reserves, and (ii) determining species diversity, species richness and abundance of small mammals in remnant bushland adjacent to sub-divisions with varying regulations governing cat husbandry. Radio tracking results to assess cat roaming patterns showed substantial variation in home range size between cats in high density suburbia (ranged between 0.01 ha – 0.64 ha) and those in low density suburbia (ranged from 0.07 ha – 2.86ha). Larger home range sizes of cats in the rural areas (up to 2.9 ha) suggest buffer zones of up to 500 metres around nature reserves are needed to exclude almost all roaming cats. The abundance and species richness of small mammals were investigated in four areas of remnant bushland. Two were adjacent to subdivisions where cat ownership was unrestricted, one next to a subdivision where cat ownership was prohibited and the remaining one next to a subdivision where compulsory night curfew and bells on pet cats were enforced. No definitive evidence of predatory impact by pet cats on the small mammals was found. Mammal species diversity was not significantly different between sites and species richness and absolute abundance were not higher in sites where cats were restricted. Vegetation comparisons showed significant differences in the structure and species composition of the vegetation between most sites and the mammal species richness and abundance appeared linked to ground cover density in the various sites. This factor, not cat restrictions, appeared to be the primary determinant of species richness, species diversity and absolute numbers of small mammals in these sites. This study in the City of Armadale has shown that the implementation of proposed cat legislation must have a “whole of ecosystem” approach, i.e. protecting identified remnant bushland containing biodiversity from threatening processes such as plant disease and inappropriate fire, especially arson, as well as possible predations from pet cats. Habitat restoration and protection may be more important conservation activities than regulation of cats. Regulation of cats can be done at differing levels of intensity and cost, bearing in mind that this community is receptive to regulation of some aspects of cat ownership. Community education on the values of cat confinement in regards to cat welfare might increase chances of compliance.

Cat ownership in Australia is declining compared to an increasing trend of cat ownership in the United Kingdom, United States and Europe. The decline in Australia may be linked to concerns over perceived impacts of cat predation and an associated dislike of cats. However, while there are numerous studies on feral cats and their impacts on declining native fauna, the impact of pet cats on suburban wildlife or fauna in remnant bushland is relatively unknown although there is a wide perception of risk. The primary aim of this thesis was to apply the precautionary principle to the question of the putative impact of pet cats on the abundance and diversity of small mammals in urban bushland adjacent to low-density suburbia in the City of Armadale, a municipality on the south-east fringe of Perth, Western Australia. At the time of writing, Western Australia is yet to introduce state legislation governing cat control although many local councils within the state have either implemented or are in the process of implementing cat regulations. The precautionary principle was deemed an ideal approach to this question, because it provides a rationale for deciding on possible actions where both the potential risk to environmental values and the uncertainty about possible impacts are high. In such cases the precautionary principle requires two broad lines of action: firstly, detailed consultation with stakeholders to determine their perceptions of risk and the actions they are prepared to take to reduce it and, secondly, research to reduce uncertainty. With regard to stakeholder consultation, local residents were surveyed in regard to their attitudes and current cat husbandry practices. A substantial proportion of respondents within this municipality believed cat regulations were necessary (75% of owners and 95% of non-owners). At least 70% of both owners and non-owners agreed with the propositions that cats not owned by licensed breeders should be desexed, local councils should restrict the maximum number of cats that can be owned on one property and that pet cats entering nature reserves are harmful to wildlife. Most (c.85%) cat owners agreed that they would license their cats if that became compulsory. Although fewer owners (c.60%) were prepared to keep their cats on their property at all times to protect wildlife, over 80% were willing to confine their cats at night if it was required. Owners seemed to be substantially motivated by the value of these measures in reducing injury to cats and facilitating the return of lost animals rather than concern over wildlife protection. Attempts to reduce uncertainty involved (i) assessing roaming patterns of pet cats to determine the sizes of appropriate buffer zones around nature reserves, and (ii) determining species diversity, species richness and abundance of small mammals in remnant bushland adjacent to sub-divisions with varying regulations governing cat husbandry. Radio tracking results to assess cat roaming patterns showed substantial variation in home range size between cats in high density suburbia (ranged between 0.01 ha - 0.64 ha) and those in low density suburbia (ranged from 0.07 ha - 2.86ha). Larger home range sizes of cats in the rural areas (up to 2.9 ha) suggest buffer zones of up to 500 metres around nature reserves are needed to exclude almost all roaming cats. The abundance and species richness of small mammals were investigated in four areas of remnant bushland. Two were adjacent to subdivisions where cat ownership was unrestricted, one next to a subdivision where cat ownership was prohibited and the remaining one next to a subdivision where compulsory night curfew and bells on pet cats were enforced. No definitive evidence of predatory impact by pet cats on the small mammals was found. Mammal species diversity was not significantly different between sites and species richness and absolute abundance were not higher in sites where cats were restricted. Vegetation comparisons showed significant differences in the structure and species composition of the vegetation between most sites and the mammal species richness and abundance appeared linked to ground cover density in the various sites. This factor, not cat restrictions, appeared to be the primary determinant of species richness, species diversity and absolute numbers of small mammals in these sites. This study in the City of Armadale has shown that the implementation of proposed cat legislation must have a 'whole of ecosystem' approach, i.e. protecting identified remnant bushland containing biodiversity from threatening processes such as plant disease and inappropriate fire, especially arson, as well as possible predations from pet cats. Habitat restoration and protection may be more important conservation activities than regulation of cats. Regulation of cats can be done at differing levels of intensity and cost, bearing in mind that this community is receptive to regulation of some aspects of cat ownership. Community education on the values of cat confinement in regards to cat welfare might increase chances of compliance.

Cat ownership in Australia is declining compared to an increasing trend of cat ownership in the United Kingdom, United States and Europe. The decline in Australia may be linked to concerns over perceived impacts of cat predation and an associated dislike of cats. However, while there are numerous studies on feral cats and their impacts on declining native fauna, the impact of pet cats on suburban wildlife or fauna in remnant bushland is relatively unknown although there is a wide perception of risk. The primary aim of this thesis was to apply the precautionary principle to the question of the putative impact of pet cats on the abundance and diversity of small mammals in urban bushland adjacent to low-density suburbia in the City of Armadale, a municipality on the south-east fringe of Perth, Western Australia. At the time of writing, Western Australia is yet to introduce state legislation governing cat control although many local councils within the state have either implemented or are in the process of implementing cat regulations. The precautionary principle was deemed an ideal approach to this question, because it provides a rationale for deciding on possible actions where both the potential risk to environmental values and the uncertainty about possible impacts are high. In such cases the precautionary principle requires two broad lines of action: firstly, detailed consultation with stakeholders to determine their perceptions of risk and the actions they are prepared to take to reduce it and, secondly, research to reduce uncertainty. With regard to stakeholder consultation, local residents were surveyed in regard to their attitudes and current cat husbandry practices. A substantial proportion of respondents within this municipality believed cat regulations were necessary (75% of owners and 95% of non-owners). At least 70% of both owners and non-owners agreed with the propositions that cats not owned by licensed breeders should be desexed, local councils should restrict the maximum number of cats that can be owned on one property and that pet cats entering nature reserves are harmful to wildlife. Most (c.85%) cat owners agreed that they would license their cats if that became compulsory. Although fewer owners (c.60%) were prepared to keep their cats on their property at all times to protect wildlife, over 80% were willing to confine their cats at night if it was required. Owners seemed to be substantially motivated by the value of these measures in reducing injury to cats and facilitating the return of lost animals rather than concern over wildlife protection. Attempts to reduce uncertainty involved (i) assessing roaming patterns of pet cats to determine the sizes of appropriate buffer zones around nature reserves, and (ii) determining species diversity, species richness and abundance of small mammals in remnant bushland adjacent to sub-divisions with varying regulations governing cat husbandry. Radio tracking results to assess cat roaming patterns showed substantial variation in home range size between cats in high density suburbia (ranged between 0.01 ha - 0.64 ha) and those in low density suburbia (ranged from 0.07 ha - 2.86ha). Larger home range sizes of cats in the rural areas (up to 2.9 ha) suggest buffer zones of up to 500 metres around nature reserves are needed to exclude almost all roaming cats. The abundance and species richness of small mammals were investigated in four areas of remnant bushland. Two were adjacent to subdivisions where cat ownership was unrestricted, one next to a subdivision where cat ownership was prohibited and the remaining one next to a subdivision where compulsory night curfew and bells on pet cats were enforced. No definitive evidence of predatory impact by pet cats on the small mammals was found. Mammal species diversity was not significantly different between sites and species richness and absolute abundance were not higher in sites where cats were restricted. Vegetation comparisons showed significant differences in the structure and species composition of the vegetation between most sites and the mammal species richness and abundance appeared linked to ground cover density in the various sites. This factor, not cat restrictions, appeared to be the primary determinant of species richness, species diversity and absolute numbers of small mammals in these sites. This study in the City of Armadale has shown that the implementation of proposed cat legislation must have a 'whole of ecosystem' approach, i.e. protecting identified remnant bushland containing biodiversity from threatening processes such as plant disease and inappropriate fire, especially arson, as well as possible predations from pet cats. Habitat restoration and protection may be more important conservation activities than regulation of cats. Regulation of cats can be done at differing levels of intensity and cost, bearing in mind that this community is receptive to regulation of some aspects of cat ownership. Community education on the values of cat confinement in regards to cat welfare might increase chances of compliance.

Dryland Australia has a distinctive mammal fauna that has been severely impacted by novel threats since European colonisation. I aimed to understand the defining characteristics of mammal refuges in this region. In chapter 2 I used atlas data to compare the historic and contemporary distributions of dryland marsupials. The greater bilby and common brushtail possum have substantially contracted in distribution. The bilby was more likely to occur on land without cattle grazing and with low rabbit densities, while the possum has contracted to cooler areas. In chapter 3 I focused on the MacDonnell Ranges to understand the factors protecting declining mammals. Predation was supported as a major driver of extant mammal richness and vast areas of rugged terrain provide vital refuge for dryland mammals. In chapter 4 I consider the hypothesis that trophic competition between the dingo and cat creates refuge from predation for small mammals by analysing the diets of the two predators for evidence of competition. I conclude that habitat complexity underpins the refuge and that effects of dingo predation on the cat population are of secondary importance. In chapters 5-7 I focused on the critically endangered central rock-rat (CRR). My habitat suitability maps confirmed a dramatic range contraction for this species over the last 100 years and their current association with extreme ruggedness supported the hypothesis that the impact of cat predation is mediated by habitat complexity. I established the effectiveness of camera trapping for sampling the CRR and, using this sampling tool, found that CRR occupancy was positively associated with areas burnt within the past 5 years and that cats forage less frequently in areas with dense hummock grass cover. Fire management could be used as a tool for rodent conservation in this environment. In chapter 8 I synthesise my findings and provide a framework for research on declining fauna.

Morphological data are crucial in evolutionary analyses for merging fossils into the tree of life, calibrating dating analyses and for enhancing inference of biological patterns and processes. Morphological phylogenetics is dominated by homoplastic characters, functional and developmental correlations, and also by highly subjective definitions of characters and their states, which in turn can mislead phylogeny reconstruction. A first study assessed the implications of biases among characters in Mesozoic mammals. Then, geometric morphometrics and molecular data were combined to study the systematics of kangaroos and wallabies. Finally, new methodologies using 3D morphometrics and multivariate statistical analyses were developed for phylogenetic inference.

Separated from mainland Australia by the Bass Strait, Tasmania has acted as an island preserve maintaining large populations of many mammalian species presently uncommon, rare, or extinct on mainland Australia. There are few studies of Tasmanian mammal distributions. Recent distributional maps, based on information from surveys and mammal specimens, allowed for an investigation of the species density distributions of the terrestrial mammals of Tasmania. Compilation of species' distributional information into species density distributions provides an overview as to which areas may provide the most significant habitat for the greatest number of species; what geographic variations may influence species distributions; and which regions remain least surveyed for mammalian species in Tasmania.

[Truncated abstract] In an era of emerging and resurging infectious diseases, understanding the ecological processes that influence pathogen activity and the influences of anthropogenic change to those are critical. Ross River virus (RRV, Togoviridae: Alphavirus) is a mosquito-borne zoonosis occurring in Australia with a significant human disease burden. In the southwest of Western Australia (WA) RRV is principally vectored by Aedes camptorhynchus Thomson (Diptera: Culicidae), which is halophilic. The inland southwest, the Wheatbelt region, of WA is substantially affected by an anthropogenic salinisation of agricultural land called dryland salinity, which threatens to influence transmission of this arbovirus. This study assessed the ecological impacts of dryland salinity on mosquitoes, mammalian hosts and their interactions to influence the potential for RRV transmission. Many aquatic insect taxa colonise ephemeral water bodies directly as adults or by oviposition. Using a manipulative experiment and sampling from ephemeral water bodies in the Wheatbelt, I demonstrated that salinity of water bodies can modify colonisation behaviour and the distribution of some organisms across the landscape. Halosensitive fauna selected less saline mesocosms for oviposition and colonisation. In particular, Culex australicus Dobrotworksy and Drummond and Anopheles annulipes Giles (Diptera: Culicidae), potential competitors with Ae. camptorhynchus, avoided ovipostion in saline mesocosms and water bodies in the field. This finding suggests salinity influences behaviour and may reduce interspecific interactions between these taxa and Ae. camptorhynchus at higher salinities. Using extensive field surveys of ephemeral water bodies in the Wheatbelt I found mosquitoes frequently colonised ephemeral water bodies, responded positively to rainfall, and populated smaller water bodies more densely than larger water bodies. The habitat characteristics of ephemeral water bodies changed in association with salinity. Consequently there were both direct and indirect associations between salinity and colonising mosquitoes. Ultimately the structure of mosquito assemblages changed with increasing salinity, favouring an increased regional distribution and abundance of Ae. camptorhynchus. The direct implication of this result is secondary salinisation has enhanced the vectorial potential for RRV transmission in the WA Wheatbelt. ... This thesis contributes to an emerging body of research aimed at delineating important ecological processes which determine transmission of infections disease. Collectively the findings in this study suggest dryland salinity enhances the potential for RRV activity in the Wheatbelt. Currently, human RRV notifications in the Wheatbelt do not reflect the salinity-RRV transmission potential in that area, but appear to be associated with dispersal of RRV from the enzootic coastal zone of southwest WA. I speculate dryland salinity is a determinant of potential for RRV transmission, but not activity. Dryland salinity is predicted to undergo a two to four fold expansion by 2050, which will increase the regional potential for RRV activity. Preservation and restoration of freshwater ecosystems may ameliorate the potential for transmission of RRV and, possibly, human disease incidence.

Predation by exotic predators (cats Felis catus and foxes Vulpes vulpes) is believed to be one of the factors that has contributed to the decline of medium-sized mammals in arid Australia. Other factors include habitat degradation by introduced herbivores (rabbits Oryctolagus cuniculus and grazing stock) and altered fire regimes after Aboriginal people moved into permanent settlements. In general, the impact of exotic predators on arid zone mammals is believed to be significant only when predator numbers have been elevated by increased food availability from exotic prey species (rabbits, house-mice Mus domesticus, cattle carcasses) or when native prey populations have already been dramatically reduced by competition from introduced herbivores. In much of the spinifex grasslands of the central Australian deserts, pastoralism never occurred, rabbit colonisation was extremely patchy and in some areas, traditional burning was still being practised when the extinctions commenced. None of the current models of mammalian extinctions adequately explain the declines in this environment. In this study I examined predator-prey interactions in two areas of the Tanami Desert to investigate whether predation by exotic predators may be a primary agent of extinction in its own right, capable of causing mass declines even in the absence of other human-induced perturbations. If this were the case then the following would be expected: (i) cats and foxes would eat medium-sized mammals when they are available, but be able to survive on alternative prey when mammals are scarce; (ii) populations of cats and foxes would be buffered against the declines of mammals during droughts, or would be able to recover more quickly than medium-sized mammals after droughts; (iii) medium-sized mammals would be more vulnerable to predation by cats and foxes than by dingoes Canis lupus dingo and other native predators, and (iv) there would be a correlation between the timings of the extinctions and the colonisation (or sudden increase) of cats and foxes. These predictions were investigated by monitoring the diets and relative abundance of cats, foxes and dingoes in relation to fluctuating prey availability in two areas of the Tanami Desert at latitudes separated by approximately 400 km. Mean annual rainfall is higher and more reliable in the northern study area which was situated in the centre of bilby Macrotis lagotis distribution within the Northern Territory, whereas the southern study area was located on the southern edge of the bilby�s range. Within each study area, monitoring occurred at three sites, approximately 20 km apart. Each site contained a sub-plot in each of two habitat types. Field work was conducted between September 1995 and December 1997. When the study began, the southern study area was experiencing drought conditions, however both study areas received significant rainfall in early 1997. The population dynamics of a variety of potential prey groups were monitored to examine their resilience during droughts, patterns of recolonisation after rainfall, and use of two habitat types: the ubiquitous sandplain, and the moister, nutrient enriched palaeodrainage habitat which is believed to have provided a refuge for medium-sized mammals during droughts. Native mammals were uncommon throughout the study period. Bilbies and macropods were significantly more abundant in the northern study area, and tended to occur more frequently in palaeodrainage habitat than sandplain. However, the palaeodrainage habitat did not appear to provide adequate refuge for the medium and large mammals during drought conditions in the southern study area, as they disappeared from the study sites altogether. Small mammals were significantly more abundant in the southern study area but densities remained low (less than 2% trap success) throughout the study, and showed little response to improved seasonal conditions. In contrast, the abundance and species richness of birds showed a marked increase following rainfall in the southern study area. Flocks of nomadic birds arrived within several months of drought-breaking rains, increasing the relative abundance of birds from 9.3 per km of transect in December 1996 to 49/km in July 1997. Reptiles were the most resilient prey group during the drought conditions. Both varanids and smaller reptiles were equally abundant in the wet and dry years and showed no difference in abundance between study areas. However, reptiles showed marked temperature-related patterns in activity, with many species becoming inactive in the winter months. A total of 142 cat scats, 126 fox scats and 75 dingo scats were analysed to investigate predator diets in the two study areas. Unlike cat, fox and dingo diets elsewhere in Australia (and the world), mammalian prey did not dominate. Reptile was the prey category that was most frequently consumed by cats and foxes in �summer� (October-April) and by dingoes throughout the year, and was identified as a �seasonal staple� prey type for all three predators in the Tanami Desert. When biomass of prey was taken into account, the varanids (predominantly the sand goanna Varanus gouldii) were the most important prey sustaining predators in the two study areas. Birds were an important part of the diets of cats and foxes in winter when reptiles were less active. Small mammals were consumed by cats and foxes throughout the study, in proportion to their field abundances. Invertebrates were a major component of the diets of foxes, representing 31% of prey items consumed. There was considerable overlap in the diets of the three predator species, but dingoes ate more medium (100-999 g) and large (greater than 1000 g) prey than cats and foxes did. The scarcity of medium-sized mammals in the study areas provided little opportunity to find evidence of predation events on such prey. However, bilby remains were found in two cat scats and one dingo scat in the northern study area, mulgara Dasycercus cristicauda remains occurred in several cat and fox scats from the southern study area, and there were fourteen occurrences of marsupial mole Notoryctes typhlops in predator scats during the study, primarily in fox scats. Elsewhere in Australia, there is ample evidence that cats and foxes regularly consume medium-sized mammalian prey (e.g. rabbits and ringtail possums Pseudocheirus peregrinus) when it is available. Overall cats were the most abundant eutherian predators in the two study areas, and they were significantly more abundant in the northern study area than the southern study area. Surveys revealed that cats can persist into droughts by feeding on reptilian prey. When the study commenced, cats occurred on five of the six sub-plots in the southern study area, despite six consecutive years of below-average rainfall. However, by the end of the first year, they could only be detected on one sub-plot. Recolonisation of the sites rapidly occurred after significant rainfall (260 mm in 2 months), when nomadic birds colonised the sites and provided a plentiful food source. Foxes also declined to very low densities during drought in the southern study area, but they had recolonised all sites by the winter of 1997. This coincided with the increase in abundance of birds, which became their most frequently consumed prey item. Overall, foxes were equally abundant in the two study areas, but statistical analyses revealed a significant interaction between latitude and habitat because in the southern study area foxes tended to utilise the palaeodrainage habitat more than the sandplain, whereas in the northern study area the majority of fox sign was detected in the sandplain habitat. This may have been due to the abundance of dingoes in the palaeodrainage habitat in the northern study area. Dingoes were significantly more abundant in the northern study area than the southern, where they were usually only present at one of the three sites. The northern study area had higher densities of macropods (supplementary prey for dingoes) and more reliable access to drinking water, which persisted in the palaeodrainage channels for up to 6 months after significant rain events. Dingo numbers were relatively stable throughout the study and did not increase in response to improved seasonal conditions in the southern study area in 1997. This study revealed that the distribution of foxes extends further north into the Tanami Desert than has previously been reported, and is not necessarily tied to the distribution of rabbits in the Northern Territory. Furthermore, discussion with Aboriginal people who lived a traditional lifestyle in the area until the 1940s, revealed that foxes were already present in the northern Tanami desert at that time, before the disappearance of many medium-sized mammal species. The patterns of medium-sized mammalian extinctions in the northern and western deserts between 1940 and 1960 is thus consistent with the colonisation of the fox. Although cats had been present in central Australia for at least 50 years before the mammalian declines occurred, this does not discount them from contributing to the extinction process. It is postulated that during the early decades of their colonisation of the arid interior, cat populations may have been maintained at low levels by predation from dingoes and also Aboriginal people (for whom cats were a favoured food). But between 1920 and 1960 the western deserts were depopulated of Aboriginal people, and human hunting of cats diminished. This coincided with the introduction of the dingo bounty scheme, which encouraged many Aboriginal people to continue making regular excursions into the deserts to collect dingo scalps. In this study, cat remains occurred in 9% of dingo scats, suggesting that dingoes may be an important predator of cats. Thus, there may have been an increase in the cat population between 1930 and 1960, producing a more significant impact on native mammal populations than had previously occurred. Information collected during this study was used to construct a new model of mammalian extinctions in the spinifex grasslands of central Australia that promotes predation by cats and foxes as the primary agent of extinction. The model proposes that cats and foxes will eat medium-sized mammals when they are available, but are capable of subsisting on naturally occurring alternative prey when mammals are scarce. Thus, cats and foxes can persist into drought periods by feeding on reptilian prey, which remains an abundant resource regardless of rainfall (at least during the warmer months). Predator populations eventually decline after a series of dry winters. When the drought breaks, the rapid response of nomadic birds provides a readily available food source for cats and foxes as they recolonise areas and commence breeding. Predation by cats and foxes thereby has the potential to exacerbate the declines of native prey populations during droughts and delay their recovery when seasonal conditions improve. In this way, introduced predators are capable of causing local extinctions of medium-sized mammals when populations contract during drought periods, even in the absence of introduced herbivores and altered fire regimes. Although dingoes also prey upon medium-sized mammals, dingoes did not cause extinctions of medium-sized mammals in the spinifex grasslands because (i) they are more reliant on drinking water than foxes and cats, thus waterless areas would have provided some degree of predation refugia, and (ii) their social structure and territoriality prevent high densities accumulating, even when resources are abundant. If further extinctions of medium-sized mammals (such as the bilby) are to be prevented, it may be necessary for wildlife managers to establish a series of predation refugia where fox and cat populations can be controlled without extinguishing local dingo populations. This could be achieved with a combination of predator-proof enclosures, zones in which foxes are killed through poison baiting and areas where Aboriginal people are employed to utilise traditional hunting methods to control introduced predators.

Animals in arid central Australia have undergone widespread declines and extinctions over the past century. These losses have coincided with what appears to have been a sharp shift in the fire regime, from one dominated by many small scale burns to one dominated by infrequent yet intense and widespread wildfires. In this thesis I investigate the processes by which fire affects small mammal and lizard populations in the Simpson Desert, central Australia. I live-trapped small mammals and lizards, used assays of foraging behaviour, measured rainfall, undertook vegetation surveys, tracked predator activity and sampled invertebrate abundance in burnt and unburnt habitat after prescribed burns and wildfire. I also conducted a global meta-analysis of vertebrate responses to fire to characterise the effects of fire on vertebrate diversity at a global scale. The meta-analysis revealed that at a global scale, prescribed burns significantly increase alpha diversity and decrease beta diversity compared with wildfires. In the Simpson Desert, the effects of prescribed burns were taxon-dependent, and wildfire did not have the predicted effects on either the alpha or beta diversity of lizards. Lizard responses were instead influenced by regional factors and food availability. Predator (fox and cat) activity was concentrated on burn ecotones and small mammals foraged for longer in burnt environments when their risk of predation was experimentally reduced. My findings suggest that fire effects on vertebrate diversity are context-dependent as a range of biotic and abiotic factors interact with fire to produce unexpected post-fire successional trajectories. Accordingly, there is no ‘one size fits all’ approach that can be incorporated into land management practices. There is, however, an urgent need for predator control in burnt habitats. I also propose a new state-and-transition model to help predict the short and longer term effect of wildfire on lizards in hummock grasslands.

This work is a linguistically based historical ethnography of the mammal species of the Flinders Ranges, South Australia, from pre-European times to the present day. The research was motivated by linguistic evidence in the Adnyamathanha people's language, Yura Ngawarla, for the recent existence of a number of mammals in the Flinders Ranges region. The work aims firstly to identify each species represented by those language terms and to discover the identity of other species also present in the past 200 years. Secondly, it aims to present an exhaustive ethnography of mammals for that region. This work is essentially cross-disciplinary, with research extending into the often overlapping fields of linguistics, anthropology, archaeology, applied science, historical zoology and history. Comparative linguistics, oral tradition, historical records, scientific data and sub-fossil material are used to identify the species present at European occupation and their role in traditional Aboriginal life, and in passing, to establish the former existence and distribution of those species throughout the region of the two South Australian gulfs. An inventory of extant and extinct Flinders Ranges species is established. Linguistic, ethnographic, zoological and historical data are used to estimate when species extinction occurred, and what may (or may not) have been the main factors involved. A significant outcome of this work is the documentation of a part of Aboriginal knowledge which itself was on the verge of extinction, and the affirmation of well attested Aboriginal oral tradition as an authentic 'authoritative source'. Conclusion: Prior to European occupation the Flinders Ranges had a rich mammalian fauna comprising around 60 native species. These played a significant part in Aboriginal people's diet, manufacturing industry and cultural and spiritual life. By the end of the first half century of European occupation or soon after around two thirds of the terrestrial species had vanished. The effect of these events on Aboriginal people's ability to survive in their own territory was devastating and irreversible.

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.

Female mammals play a central role in determination of social structure and are thus central to understanding the overall fission-fusion grouping pattern characteristic of many delphinid societies. Focusing specifically on female-female relatedness and association patterns, I have analysed more than 17 years of group composition, behavioural data, and genetic information to investigate complex interactions between behavioural ecology and relatedness and to also examine the common social evolutionary theory, that variation in mammalian social systems is typically attributed to five main factors: inclusive fitness, predation pressure, sexual conflict and male harassment, inbreeding avoidance, and resource competition. Overall, I found that female bottlenose dolphin association patterns depend upon the interplay between matrilineal kinship, biparental relatedness and home range overlap, and that female bottlenose dolphins seem to adapt their social strategies to seasonal variation in levels of predation and male harassment. The presence of both high sexual conflict and bisexual philopatry lead me to investigate the extent of inbreeding avoidance. I found that more than 14% of the calves were most likely the product of mating between close relatives, and identified female fitness costs to inbreeding. We were able to show that the effect of inbreeding on females??? fitness occurs via two independent mechanisms: being inbred and having at least one inbred calf. Inbred calves are on average weaned later than non-inbred calves, and a female???s first calf has a higher probability to be an inbred than subsequent calves. Last, I examined whether sociality provides inclusive fitness to female bottlenose dolphins through an investigation of both the additive genetic and social variance components of female calving success using a pedigree-free animal model. I found that variance in calving success of female bottlenose dolphins is best explained by complex genetic and social interactions. Females with high calving success showed both high genetic and social merit; they not only have good genes but also prefer to associate with others of high fitness. This study reveals that both social and heritable genetic variance contribute to fitness trait variance in the wild.

Many Australian mammal species have experienced a severe decline in range and abundance over the last 200 years. Conservation of threatened mammals involves conservation of habitat and food resources. Mycorrhizal fungi produce spore-laden sporocarps, which are consumed by many ground dwelling mammals. This interaction is called mycophagy. Clearly, fungal resources are of fundamental importance to the conservation of many mammal species in Australia. The plant pathogen Phytopthora cinnamomi has catastrophic effects on ecosystems in the Jarrah forest of Western Australia. The effects of the pathogen on flora have been extensively studied, but it's effects on mammal communities in these ecosystems has not been measured. This study investigates differences in mycophagy between P. cinnamomi affected and healthy Jarrah forest ecosystems. This was achieved by investigating relationships between measured environmental variables, fungal productivity and mycophagous tendencies at three site types in the Darling Range, near Dwellingup. A trend was apparent between biomass and diversity of hypogeous fungi between sites. Sites of low impact had the highest number of hypogeous fungi species, plus the greatest biomass of sporocarps. Sites exhibiting high P. cinnamomi impact had significantly reduced hypogeous fungal biomass and diversity. Significant differences were evident in mycophagy between Phytophthora affected ecosystems. However, this study was unable to draw definitive conclusions due to the complex nature of interactions, and differences among sites. For example, environmental variables such as litter biomass had large standard deviations, suggesting sampling effort required was very high. Clearly, longer term surveys are required to provide definitive conclusions. Trends in mycophagy were evident as a function of season. This study identified fungal utilisation by previously undocumented mycophagous mammals. Sites with medium P. cinnamomi impact had the greatest degree of mycophagy. High and Low impact sites showed similarities in the number of spores in scats. Dasyurus geoffroii consumed the greatest diversity of fungal taxa, and had the greatest number of spores in the scats. Rattus rattus consumed the second greatest number of spores, and Sminthopsis gilberti, Mus musculus and Antechinus flavipes consumed similar, low numbers of spores. The number of spore types however, was high in A. flavipes, S. gilberti and M. musculus. R. rattus exhibited very low diversity of spores in scats, however, these spore types were in high occurrence.

The honey possum Tarsipes rostratus is a tiny (7 - 12 g) highly specialised flower-feeding marsupial endemic to the south-western corner of Australia. The impact of fire on this small mammal was studied, over a 19-year period, in the Fitzgerald River National Park, a large (330,000 ha) area of relatively undisturbed heathland/shrubland, rich in the proteaceous and myrtaceous plants upon which the honey possum appears to rely for food. The honey possum is the most abundant and widespread mammal in this Park. Capture rates of honey possums were significantly related to the years since the vegetation was last burnt, annual rainfall in the preceding (but not the current) year, the season when trapping occurred, and the trapping grid operated. Capture rates declined markedly after fire and remained low (less than one third of those in long unburnt vegetation) for about 4 - 5 years following a fire. Rates of capture then increased steadily over the next 20 - 25 years, with maximal abundance recorded about 30 years after fire. Thereafter, there appeared to be a slight decline in capture rates, but even in the vegetation unburnt for longest (> 50 years since fire), honey possum abundance was substantial and relatively stable. In contrast to these changes in abundance, the structure of the honey possum population, with 79 % adults and 57 % males, appeared little influenced by fire history, annual rainfall, season or grid. The increase in the rates of capture of honey possums following fire paralleled the pattern of availability of cover in the vertical and, to a lesser extent, horizontal plane. Indeed, projective foliage cover took around 20 years after fire to reach levels similar to those available in areas unburnt for even longer. The trend in capture rates was also congruent with the maturation of the most frequently visited foodplants of honey possums, particularly Banksia nutans (summer flowering) and B. baueri (winter flowering). Areas long unburnt still contained shelter and foodplants adequate for honey possums even 50 years or more after fire, with only slight evidence of senescence. Pollen loads indicated that honey possums caught in burnt areas, where their preferred foodplants were absent, continued to feed on these favoured foodplants (Banksia and Dryandra spp.) at nearby unburnt areas. In addition, they also fed, in both burnt and long unburnt areas, upon a suite of other plant species that regenerated more rapidly from lignotubers and epicormic buds, as well as from seeds (e.g. Eucalyptus and Calothamnus spp.). Thus, honey possums appeared to persist with their preferences for feeding from a limited number of flowering plants despite some of these species not being available in recently burnt areas for many years. Nearby patches of unburnt vegetation can clearly be important refuges, feeding grounds and shelter for the few honey possums that visit recently burnt areas, and appear to be the source of honey possum colonists in the years following a fire. Capture rates were also greater following years when rainfall was higher than average. Indeed, rainfall had as great an influence upon capture rates as time since fire. Capture rates were also consistently higher over winter, and to a lesser extent over summer, than in either autumn or spring. Individual grids, even those close together in apparently similar vegetation with a similar fire history, still differed significantly overall in their capture rates of honey possums. This last finding has implications for the use of chronosequences in the study of post-fire changes in biota. Although not the primary focus of the study, data on the limited suite of other, far less abundant, small mammals present indicated that house mouse Mus musculus domesticus numbers peak soon after fire (about two years after fire), grey-bellied dunnart Sminthopsis griseoventer numbers somewhat later (about eight years after fire) and that southern bush rats Rattus fuscipes fiuscipes, like honey possums, are later successional species. Most species were present in vegetation over a range of post-fire ages, with data consistent with models based on sequential changes in relative abundance. Like many Australian mammals, the range of the honey possum has contracted substantially over the last 200 years and the coastal heathlands of the south-west are its last stronghold. In terms of its conservation, this study indicates that, if possible, management burns in these heathlands should be separated by intervals of at least 20 years between successive burns, and preferably even longer. If burns are required more frequently to meet other management priorities, it is highly preferable that they are small and patchy, rather than large scale. Such practices may help ensure the long-term survival of this unique, highly specialised and endemic marsupial.

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.

The Gilbert’s potoroo (Potorous gilbertii) is a small marsupial endemic to the Two Peoples Bay Nature Reserve in the south-west of Western Australia. The Gilbert’s potoroo is classified as Australia’s most critically endangered mammal (IUCN 2006) with an estimated population of only 35 individuals. This thesis examines the health and disease status of the Gilbert’s potoroo, presenting a strong case for the relatively new concept of disease as a potential threatening factor and modifier of population decline. Specific diseases, including Cryptococcus, ectoparasitism, endoparasitism, haemoparasitism, Toxoplasma and a novel Treponema organism are extensively studied. An assessment of the clinical significance of these diseases is made, and management strategies are recommended to minimise the impact of these diseases on both the wild and captive population. The novel Treponema organism which clinically presents with tenacious, green discharge and an associated balanoposthitis in males is molecularly characterized. Epidemiological studies show the effects of this agent on reproductive function and a penicillin-based treatment regime is trialled in the analogous long-nosed potoroo (Potorous tridactylus) with a recommendation to then trial this treatment regime in the critically endangered Gilbert’s potoroo. Standard haematological and urinalysis findings are tabulated to form reference ranges for this species. A treatment regime for Cryptococcus in the analogous long-nosed potoroo is reported and parasitological findings, including the identification of a novel tick species are discussed. This thesis addresses key health issues, which have subsequently been incorporated into the Recovery Plan of the Gilbert’s potoroo. A document encompassing multiple disciplines and expertise to support the recovery of this critically endangered marsupial in its current environment. In addition, this thesis outlines a recommended health monitoring and treatment protocol for future translocation procedures and provides a working example of the emerging importance of health monitoring in threatened species recovery programs.

The Gilbert's potoroo (Potorous gilbertii) is a small marsupial endemic to the Two Peoples Bay Nature Reserve in the south-west of Western Australia. The Gilbert's potoroo is classified as Australia's most critically endangered mammal (IUCN 2006) with an estimated population of only 35 individuals. This thesis examines the health and disease status of the Gilbert's potoroo, presenting a strong case for the relatively new concept of disease as a potential threatening factor and modifier of population decline. Specific diseases, including Cryptococcus, ectoparasitism, endoparasitism, haemoparasitism, Toxoplasma and a novel Treponema organism are extensively studied. An assessment of the clinical significance of these diseases is made, and management strategies are recommended to minimise the impact of these diseases on both the wild and captive population. The novel Treponema organism which clinically presents with tenacious, green discharge and an associated balanoposthitis in males is molecularly characterized. Epidemiological studies show the effects of this agent on reproductive function and a penicillin-based treatment regime is trialled in the analogous long-nosed potoroo (Potorous tridactylus) with a recommendation to then trial this treatment regime in the critically endangered Gilbert's potoroo. Standard haematological and urinalysis findings are tabulated to form reference ranges for this species. A treatment regime for Cryptococcus in the analogous long-nosed potoroo is reported and parasitological findings, including the identification of a novel tick species are discussed. This thesis addresses key health issues, which have subsequently been incorporated into the Recovery Plan of the Gilbert's potoroo. A document encompassing multiple disciplines and expertise to support the recovery of this critically endangered marsupial in its current environment. In addition, this thesis outlines a recommended health monitoring and treatment protocol for future translocation procedures and provides a working example of the emerging importance of health monitoring in threatened species recovery programs.

The Gilbert’s potoroo (Potorous gilbertii) is a small marsupial endemic to the Two Peoples Bay Nature Reserve in the south-west of Western Australia. The Gilbert’s potoroo is classified as Australia’s most critically endangered mammal (IUCN 2006) with an estimated population of only 35 individuals. This thesis examines the health and disease status of the Gilbert’s potoroo, presenting a strong case for the relatively new concept of disease as a potential threatening factor and modifier of population decline. Specific diseases, including Cryptococcus, ectoparasitism, endoparasitism, haemoparasitism, Toxoplasma and a novel Treponema organism are extensively studied. An assessment of the clinical significance of these diseases is made, and management strategies are recommended to minimise the impact of these diseases on both the wild and captive population. The novel Treponema organism which clinically presents with tenacious, green discharge and an associated balanoposthitis in males is molecularly characterized. Epidemiological studies show the effects of this agent on reproductive function and a penicillin-based treatment regime is trialled in the analogous long-nosed potoroo (Potorous tridactylus) with a recommendation to then trial this treatment regime in the critically endangered Gilbert’s potoroo. Standard haematological and urinalysis findings are tabulated to form reference ranges for this species. A treatment regime for Cryptococcus in the analogous long-nosed potoroo is reported and parasitological findings, including the identification of a novel tick species are discussed. This thesis addresses key health issues, which have subsequently been incorporated into the Recovery Plan of the Gilbert’s potoroo. A document encompassing multiple disciplines and expertise to support the recovery of this critically endangered marsupial in its current environment. In addition, this thesis outlines a recommended health monitoring and treatment protocol for future translocation procedures and provides a working example of the emerging importance of health monitoring in threatened species recovery programs.

La reconnaissance joue un rôle important dans les systèmes de communication animale et plusieurs modalités sensorielles sont impliquées à cette fin. Bien que la reconnaissance mère-jeune ait été largement étudiée, il y a un manque d'information sur la reconnaissance multimodale et l'importance relative des différentes modalités dans ce processus. Dans cette thèse, j'ai exploré la communication multimodale chez un mammifère colonial - le lion de mer Australien (Neophoca cinerea). La reconnaissance mère-jeune est connue pour être multimodale chez cette espèce, mais les processus sous-jacents de la reconnaissance olfactive et visuelle, ainsi que les interactions entre les indices acoustiques, visuels et olfactifs, et leurs contributions relatives restent inconnues. Des analyses chimiques ont permis de déterminer si les profils chimiques diffèrent selon le sexe et l'âge, les colonies et les régions corporelles des animaux. La présence de similarités chimiques entre la mère et son petit suggèrent que l'appariement des phénotypes pourrait être utilisé pour la reconnaissance olfactive. J'ai examiné le rôle des indices visuels lors de la reconnaissance mère-jeune et j'ai constaté que les indices visuels spécifiques à l'âge sont utilisés par les femelles pour affiner la recherche de leur petit dans la colonie. Les jeunes ont également la capacité de distinguer divers indices visuels, qui peuvent être utilisés pour identifier les différentes classes de congénères. Enfin, j’ai pu aussi déterminer comment les indices acoustiques, olfactifs et visuels sont utilisés de manière synergique dans le processus d’identification individuel, et les résultats sont interprété dans une perspective coûts-avantages pour démêler les pressions évolutives sur chaque composante de ce système de communication. Si les différents indices sensoriels ont la capacité de transmettre des informations en isolation, leur rôle peut être différent lorsque d'autres indices sensoriels sont présents. Les résultats de cette recherche fournissent des résultats sans précédent, contribuant à une meilleure compréhension de la reconnaissance mère-jeune chez les mammifères, ainsi que des règles générales de communication chez les vertébrés
Recognition plays an important role in animal communication systems and individuals often employ different sensory modalities to enact this activity. Although recognition has been widely investigated, especially for mother-offspring interactions, there is a dearth of information about multimodal recognition and the relative importance and interactions of various sensory cues. In this thesis, I explored multimodal communication in a colonial mammal – the Australian sea lion (Neophoca cinerea). Communication during mother-pup reunions is known to be multimodal in this species, yet the underlying processes of olfactory and visual recognition, as well as the interactions between acoustic, visual and olfactory cues remain unclear. Through chemical analyses, I determined whether chemical profiles differ among sex and age classes, colonies, and body regions of animals. Chemical similarities between mothers and pups indicate that phenotype matching may be used by Australian sea lions for olfactory recognition. I examined the role of visual cues in mother-pup recognition and found that age-specific visual cues assist mothers to refine their search for their offspring in the colony. Pups are capable of distinguishing various visual cues that can be used in the assessment of conspecifics. Having provided baseline information about the role of sensory cues in isolation, I determined how acoustic, olfactory, and visual cues are used in a synergistic way to ensure accurate mutual recognition and then interpreted the results using a cost-benefit perspective to disentangle the evolutionary pressures on each component of this communication system. I showed that although cues have the ability to convey given information in isolation, their role may be different when other sensory cues are present. Furthermore, there is a mutual dependency in the communication system, where the limitations imposed on one participant of the dyad affect cue use by the other. These findings contribute to a better understanding of mammal mother-offspring recognition and communication mechanisms in vertebrates

[Truncated abstract] Understanding the effect that the disturbance of habitat by humans has on the population dynamics and ecology of wild animals is critical for the management of these populations. By understanding the demographic effects of disturbance the ways in which a population can be managed to increase or decrease its rate of change in size also become apparent. This thesis describes the effect that human disturbance, through the establishment of a large naval base, has had on the population dynamics and ecology of tammar wallabies (Macropus eugenii) on Garden Island, Western Australia. The disturbance of the environment on the HMAS Stirling Naval Base included the establishment of large areas of irrigated and fertilised couch grass (Cynodon dactylon) that increased and made virtually constant the amount of food available to the tammars in that area. In addition, traffic associated with the naval base resulted in large numbers of tammar wallabies being killed by vehicles. The effects of these disturbances were determined by comparing population dynamics, through vital rates of survival and fecundity and population growth rates, and spatial ecology, through the size of the animals' home ranges, in three areas of Garden Island. The three areas were the naval base (highly disturbed), southern bushland (adjacent to the naval base) and the northern bushland (undisturbed). The tammars on the naval base were in better body condition than those living in the two bushland areas of the island. ... When the impact of road-kills was removed, increased to 1.150.101 per year on the naval base and 0.960.076 per year in the southern bushland. Fecundity transitions, defined as the product of the rates of birth and pouch-young survival, and adult survival rates were lower in the bushland areas compared with the naval base in two of the three years, which were the main reasons for the lower estimates. There were no significant differences in the size of the tammars' home ranges between areas with modified or unmodified habitats or between the sexes (P>0.05). In summer the mean size of the home ranges was 3.90.66 ha, which was larger than winter when home ranges were 3.20.54 ha, but this difference failed to reach significance (P=0.058). These results indicate that the modification of the tammars' habitat has probably not caused significant changes in the size of the animals' home ranges. The size of the home ranges of tammar wallabies is likely to be determined by a complex interaction of many factors, and habitat modification alone has not been sufficient to cause substantial changes. The results presented in this thesis demonstrate that the disturbance caused by the establishment of the naval base on Garden Island has altered the population dynamics of the tammars wallabies, through increasing in the amount of food available to the tammars and through high numbers of road-kills. These results also demonstrate how gaining detailed knowledge of population dynamics can have direct application to managing the impact of disturbance on populations of wild animals.

Translocations to closed systems such as fenced reserves are commonly used for the conservation of threatened fauna species worldwide and although fenced reserves can provide significant conservation benefits to biodiversity, they can also bring forth potential threats. Ecologically similar species can stably coexist by partitioning resources along at least one of three niche dimensions (food, space, or time), thereby reducing interspecific competition. However, resources are limited in fenced reserves and natural processes that regulate populations in response to resource availability, such as dispersal into surrounding areas, are unable to occur. Consequently, there is increased potential for competition because there are less resources available for partitioning. Furthermore, the removal of predators and competitors, both native and introduced, can increase the risk of overpopulation due to a reduction in the incidence of density-dependant mortality. This can potentially lead to overuse of resources and further increase the potential for competition. Interspecific competition may lead to the decline or exclusion of a more sensitive species by a less sensitive species. Such interactions are difficult to predict, especially as many threatened species no longer naturally co-exist in their current ranges or are poorly studied. I investigated resource use of two potentially competing native marsupials, boodies (Bettongia lesueur) and mala (Lagorchestes hirsutus), that co-exist in a 1100 ha predator-free fenced reserve located in the arid rangelands of central Western Australia. Resource overlap between coexisting populations of these two species has not been studied previously, but the literature suggests the potential for considerable dietary overlap. I investigated the degree of dietary overlap using scat DNA from non-invasively collected scats, as well as the degree of spatial overlap using scat counts and temporal overlap using camera traps. Boom-bust dynamics have been observed in the Matuwa boodie population (and elsewhere), which raised the concern of subsequent suppression of the potentially less competitive mala. The suppression of mala however cannot be confirmed because there are currently no effective methods to monitor the population size of this elusive species at Matuwa. Therefore, I also trialled non-invasive DNA-based sampling methods using field-collected scats to estimate the abundance of the Matuwa mala population. This method has not been used on mala previously. Results from the dietary analyses suggest there is potential for significant exploitative competition, as both species’ scats consisted of a high percentage of Acacia spp. However, the Acacia DNA could not be identified to species level and there are at least 19 Acacia species within the enclosure, so it is unknown which species they are consuming, and further studies are necessary to resolve the extend of overlap. Additionally, boodies also consumed a much higher proportion of fungi than mala, which may reduce the extent of overall dietary overlap, thereby reducing the potential for resource competition. The species displayed no sign of significant spatial or temporal avoidance at a broad scale, possibly because dietary partitioning exists so there is limited risk from using the same habitats and having similar activity rhythms. The results however, suggest the potential for fine scale spatial and temporal avoidance; this should be investigated further. This study successfully used non-invasively collected scat DNA to identify individuals and estimate the abundance of the mala population at Matuwa. Spatially explicit capture recapture (SECR) and mark-resight models estimated a population size of over 110 individuals. With refined scat collection methods, DNA-based sampling will be an effective and valuable method for monitoring mala. This is a significant outcome because current methods have limited success with the elusive species, but it is essential the few remaining mala populations are effectively monitored to prevent further decline. The information gained from this study will contribute to the successful conservation of boodies and mala by adding to existing knowledge and providing insight into the ability of these species to coexist. Finally, this study will contribute to gaining a better understanding of resource use by small mammals and how they partition resources (including food, space and time) in a closed environment where resources are significantly more limited than the wider landscape.

The site fidelity of humpback and southern right whales in Algoa Bay was investigated as a baseline study to examine the importance of this area for the future conservation of these species. An absence of whales since the 1980’s from Algoa Bay and more frequent sightings of southern right and humpback whales during a survey conducted between 2008 and 2011 in Algoa Bay led to the present photo-identification study. Data were collected from boat-based surveys along the coastline in 2015 and 2016 and data from a previous boat-based study during 2008-2011 assessing the occurrence of all cetaceans in Algoa Bay were added. A cumulative number of 96 individual southern right whales and 184 individual humpback whales were identified from callosity patterns and dorsal fins, respectively, over this period in Algoa Bay. A low resighting rate for both species was observed within (6.25 for southern right whales & 6.98% for humpback whales) and between years (1.04% for southern right whales & 9.24% for humpback whales) with mainly individual adult humpback whales being resighted. In contrast, all southern right whale resightings were confirmed to be mother-calf pair individuals. The timing of monthly sightings and resightings of mother-calf pair individuals in the bay may suggest that this area may serve as a fairly new nursery area for southern right whales and as a possible migratory corridor for humpback whales during their migrations to and from their breeding grounds. The sighting distribution within the bay suggest that mother-calf pairs are located closer inshore and further away from the shipping activities on the eastern side of the bay in the proximity of two operational ports. This forms an important baseline for future monitoring to assess the effect of increased shipping activity in the bay on the breeding behaviour of the whales. The site fidelity of humpback and southern right whales in Algoa Bay was investigated as a baseline study to examine the importance of this area for the future conservation of these species. An absence of whales since the 1980’s from Algoa Bay and more frequent sightings of southern right and humpback whales during a survey conducted between 2008 and 2011 in Algoa Bay led to the present photo-identification study. Data were collected from boat-based surveys along the coastline in 2015 and 2016 and data from a previous boat-based study during 2008-2011 assessing the occurrence of all cetaceans in Algoa Bay were added. A cumulative number of 96 individual southern right whales and 184 individual humpback whales were identified from callosity patterns and dorsal fins, respectively, over this period in Algoa Bay. A low resighting rate for both species was observed within (6.25 for southern right whales & 6.98% for humpback whales) and between years (1.04% for southern right whales & 9.24% for humpback whales) with mainly individual adult humpback whales being resighted. In contrast, all southern right whale resightings were confirmed to be mother-calf pair individuals. The timing of monthly sightings and resightings of mother-calf pair individuals in the bay may suggest that this area may serve as a fairly new nursery area for southern right whales and as a possible migratory corridor for humpback whales during their migrations to and from their breeding grounds. The sighting distribution within the bay suggest that mother-calf pairs are located closer inshore and further away from the shipping activities on the eastern side of the bay in the proximity of two operational ports. This forms an important baseline for future monitoring to assess the effect of increased shipping activity in the bay on the breeding behaviour of the whales.

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The South American fur Seal, Arctocephalus australis, is distributed along Southern Hemisphere coast with breeding colonies located since Peru until Uruguay. This work focuses on the Atlantic ESU and covers most of the colonies of the Atlantic coast. In recent past, several colonies underwent strong size reduction with hunting and El Niño events. Most studies have focused on investigate the Pacific ESU, little being known about the Atlantic populations. The population structure and genetic variability in this area were assayed with mitochondrial DNA control region and eleven microsatellite loci. The results found high levels of genetic diversity in the region, without evidence of recent genetic bottleneck but with evidence of a population expansion around 200-100 thousand years ago. A sign of genetic structure were found between colonies from Uruguay and Chubut when evaluated by the mtDNA. This is likely due to their strong female philopatry. However, microsatellite analysis did not revealed any existing structure, even between distant areas, supporting that most gene flow is mediated by males. For conservation purposes, these results shows that the South American fur seal Atlantic ESU is a single population and because of that, conservation measures should be aligned among the countries of its distribution.
O lobo-marinho sul-americano, Arctocephalus australis, está distribuído ao longo da costa do hemisfério sul com colônias reprodutivas localizadas desde o Peru até o Uruguai. Este trabalho foca na UES do Atlântico e cobre a maioria de suas colônias. No passado recente, várias colônias sofreram drásticas reduções populacionais com a caça e os eventos de El Niño. Muitos estudos focaram na análise da UES do Pacífico, no entanto, pouco se sabe sobre a UES do Atlântico. Neste estudo a estrutura populacional e a variabilidade genética destas populações foram avaliadas através da região controle do DNA mitocondrial e 11 loci de microssatélites. Os resultados encontraram alto nível de diversidade genética nesta região, sem sinal de gargalo genético recente, mas com sinais de uma expansão populacional iniciada entre 200. 000 e 100. 000 anos atrás. Um sinal de estruturação foi encontrado entre as colônias do Uruguai e Chubut quando avaliado a partir do DNA mitocondrial, provavelmente causado pela forte filopatria das fêmeas. No entanto, a análise de microssatélite não revelou a existência de estruturação, mesmo entre as diversas subpopulações mais distantes, sugerindo que o fluxo gênico seja mediado pelos machos. Para fins de conservação, estes resultados mostram que o lobo-marinho sul-americano da UES do Atlântico é uma única população, e por causa disso, medidas de segurança devem ser alinhadas entre os países de sua distribuição.

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O lobo-marinho sul-americano, Arctocephalus australis, est? distribu?do ao longo da costa do hemisf?rio sul com col?nias reprodutivas localizadas desde o Peru at? o Uruguai. Este trabalho foca na UES do Atl?ntico e cobre a maioria de suas col?nias. No passado recente, v?rias col?nias sofreram dr?sticas redu??es populacionais com a ca?a e os eventos de El Ni?o. Muitos estudos focaram na an?lise da UES do Pac?fico, no entanto, pouco se sabe sobre a UES do Atl?ntico. Neste estudo a estrutura populacional e a variabilidade gen?tica destas popula??es foram avaliadas atrav?s da regi?o controle do DNA mitocondrial e 11 loci de microssat?lites. Os resultados encontraram alto n?vel de diversidade gen?tica nesta regi?o, sem sinal de gargalo gen?tico recente, mas com sinais de uma expans?o populacional iniciada entre 200.000 e 100.000 anos atr?s. Um sinal de estrutura??o foi encontrado entre as col?nias do Uruguai e Chubut quando avaliado a partir do DNA mitocondrial, provavelmente causado pela forte filopatria das f?meas. No entanto, a an?lise de microssat?lite n?o revelou a exist?ncia de estrutura??o, mesmo entre as diversas subpopula??es mais distantes, sugerindo que o fluxo g?nico seja mediado pelos machos. Para fins de conserva??o, estes resultados mostram que o lobo-marinho sul-americano da UES do Atl?ntico ? uma ?nica popula??o, e por causa disso, medidas de seguran?a devem ser alinhadas entre os pa?ses de sua distribui??o

Invasive predators are major drivers of global biodiversity loss and their impacts may be worsened by other disturbances such as fire. I examined how the fire history of shrublands influences the ecology of feral cats Felis catus, dingoes Canis dingo and their prey species in Western Australia’s northern Wheatbelt region. A review of the literature revealed that feral cats inhabit a diverse range of ecosystems worldwide, but are generally recorded most often in habitat types characterised by a mixture of plant growth forms close to ground level. Cat habitat use is influenced by predation/competition, prey availability, shelter availability and anthropogenic resource subsidies. Relatively few studies were available for review and the strength of evidence contained within them was generally low, which highlighted the need for more rigorous field studies. I examined overlap in resource use between cats and dingoes using remote camera surveys and dietary analysis of scats. Both carnivores were recorded in all four major habitat types: recently burnt shrublands (10 to 14 years since last fire), long unburnt shrublands (34 to ~49 years), very long unburnt shrublands (> 50 years), and woodlands. Dingoes and cats preferred woodlands and very long unburnt shrublands respectively, but spatial overlap between the two species was still common. Mean diurnal activity time for feral cats was two and a half hours later than that of dingoes. The diet of feral cats was more diverse than that of dingoes and dietary overlap between the two carnivores was relatively low. Rabbit remains did occur relatively frequently in both cat and dingo scats, but small mammals, reptiles and birds were also common in cat scats, and macropods in dingo scats. Nine of the 15 prey species studied showed a preference for either recently burnt or long unburnt shrublands. Two small mammals and three reptiles were most abundant in recently burnt areas, while the abundance of one small mammal and three reptiles was highest in long unburnt areas. Using giving up density experiments, I showed that rodents exhibited differential foraging behaviour in the two vegetation fire ages. The rodents foraged for longer in sheltered compared to open microhabitats, but this pattern only occurred in recently burnt, not long unburnt shrublands, probably because the higher density of understorey vegetation in recently burnt areas provided the rodents with extra cover to hide and escape from predators. I also developed a new framework for conceptualising interactions between invasive predators and other ecological disturbances, such as fire, habitat fragmentation, and top -predator decline. The impacts of invasive predators can be classified as either functional (density -independent) or numerical (density -dependent), and they interact with other threats through both habitat -mediated (fire, grazing, land clearing) and community -mediated (top -predator decline, altered prey populations, anthropogenic resource subsidies) interaction pathways. The key findings of this thesis show that both old and young shrublands can be suitable habitat for feral cats; predator -prey dynamics are influenced by successional habitat stages; small mammals show behavioural, as well as population -level responses to fire; and that invasive predator management is likely to benefit from addressing multiple threats in unison.

At Cape Gantheaume, Kangaroo Island (South Australia), adult male, lactating female and juvenile New Zealand (NZ) and Australian fur seals regularly return to the same colony, creating the potential for intra- and inter-specific foraging competition in nearby waters. I hypothesised that these demographic groups would exhibit distinct foraging strategies, which reduce competition and facilitate their coexistence. I analysed the diet of adult male, adult female and juvenile NZ fur seals and adult male Australian fur seals and studied the diving behaviour of adult male and lactating female NZ fur seals and the at-sea movements of juvenile, adult male and lactating female NZ fur seals. Female diet reflected that of a generalist predator, influenced by prey availability and their dependant pups� fasting abilities. In contrast, adult male NZ and Australian fur seals used larger and more energy-rich prey, most likely because they could more efficiently access and handle such prey. Juvenile fur seals primarily utilised small lantern fish, which occur south of the shelf break, in pelagic waters. Juveniles undertook the longest foraging trips and adult males conducted more lengthy trips than lactating females, which perform relatively brief trips in order to regularly nurse their pups. Unlike lactating females, some adult males appeared to rest underwater by performing dives that were characterised by a period of passive drifting through the water column. The large body sizes of adult males and lactating females facilitated the use of both benthic and pelagic habitats, but adult males dived deeper and for longer than lactating females, facilitating vertical separation of their foraging habitats. Spatial overlap in foraging habitats among the age/sex groups was minimal, because lactating females typically utilised continental shelf waters and males used deeper water over the shelf break, beyond female foraging grounds. Furthermore, juveniles used pelagic waters, up to 1000 km south of the regions used by lactating females and adult males. The age and sex groups in this study employed dramatically different strategies to maximise their survival and reproductive success. Their prey and foraging habitats are likely to be shaped by body size differences, which determine their different physiological constraints and metabolic requirements. I suggest that these physiological constraints and the lactation constraints on females are the primary factors that reduce competition, thereby facilitating niche partitioning.

Assessment of trophic interactions between increasing populations of New Zealand fur seals (Arctocephalus forsteri) and fisheries in southern Australia is limited due to a lack of species specific demographic data and an understanding of the factors influencing population growth. To establish species specific demographic parameters a cross-sectional sample of New Zealand fur seal females (330) and males (100) were caught and individually-marked on Kangaroo Island, South Australia between 2000 and 2003. The seals were aged through examination of a postcanine tooth, which was removed from each animal to investigate age-specific life-history parameters. Annual formation of cementum layers was confirmed and accuracy in age estimation was determined by examination of teeth removed from individuals of known-age. Indirect methods of assessing reproductive maturity based on mammary teat characteristics indicated that females first gave birth between 4-8 years of age, with an average age at reproductive maturity of 5 years. Among reproductively mature females, age-specific reproductive rates increased rapidly between 4-7 years of age, reaching maximum rates of 70-81% between 8-13 years, and gradually decreased in older females. No females older than 22 years were recorded to pup. Age of first territory tenure in males ranged from 8-10 years. The oldest female and male were 25 and 19 years old, respectively. Post-weaning growth in females was monophasic, characterised by high growth rates in length and mass during the juvenile growth stage, followed by a gradual decline in growth rates after reproductive maturity. In contrast, growth in males was biphasic and displayed a secondary growth spurt in both length and mass, which coincided with sexual and social maturation, followed by a rapid decline in growth rates. Age-specific survival rates were high (0.823-0.953) among prime-age females (8-13 yrs of age) and declined in older females. Relative change in annual pup production was strongly correlated with reproductive rates of prime-age females and adult female survival between breeding seasons.

Snow is an important factor in the lives of flora and fauna in those regions where it occurs. Despite this, there is a relative lack of information about the ecological role of snow. In addition, on a global scale the majority of the research on snow ecology has been based in the boreal regions of North America and Eurasia. Insights from these areas may not extrapolate well to Australia. The distribution and physical characteristics of snow are highly variable both temporally and spatially. Its occurrence is affected by a range of factors acting at multiple scales. Working in snow covered areas, however, presents considerable practical problems, particularly for researchers attempting to sample organisms in the subnivean space between the base of the snowpack and the ground surface. As a result, most research has focused on small-scale projects because of logistical and animal-welfare issues. A technique was developed for this study for sampling small mammals beneath the snow using hairtubes fitted with bait and a removable adhesive surface that could be inserted into the subnivean space through a vertical PVC pipe. The technique provided a 39% detection rate with only 0.2% of tubes visited but not collecting hair samples. Using. this technique, it was possible to expand systematic sampling of small mammals in the subnivean space to larger scales at which snow cover can vary spatially and temporally particularly at the landscape scale. The main part of this research was conducted over two winters (2002-2003) at sites established in a series of valleys close to the Summit Road in Kosciuszko National Park, south-eastern Australia. Selection of sites was based on factors considered important in influencing the distribution of snow in the landscape and representative of the key vegetation types occurring in the subalpine zone. The resulting design consisted of 72 sites stratified by elevation (1501-1600 m, 1601-1700 m, 1701-1800 m), aspect (accumulating, ablating) and vegetation type (woodland, wet heath, dry heath, grassland) with each combination replicated three times. Each site consisted of three hairtube plots approximately 10 metres apart, at which small mammals were sampled. In addition, a range of biotic and abiotic factors including snow cover characteristics were measured throughout the winter at these same sites. In January 2003, a major bushfire burned 70% of the subalpine area of Kosciuszko National Park and damaged 83% of the sites established in 2002. As a result sampling during winter 2003 was limited to high elevation sites, along with a fifth habitat type (boulderfields). The snow cover that occurs in the main alpine and subalpine region of the· Snowy Mountains is primarily maritime in areas where there is sufficient accumulation, and ephemeral at lower elevations and ort higher ablating aspects. Maritime snow is generally deep (> lOOcm), with a density >0.30gcm-3, as a result of destructive metamorphism throughout the winter. The formation of depth hoar, which is considered to be important in acilitating the development of the subnivean space, does not occur under these conditions. Ephemeral snow is characterised by warm shallow snow that often melts before new snow is deposited. When snow was present, detections of dusky antechinus, Antechinus swainsonii and the bush rat, Rattus fuscipes were negatively correlated with snow depth and duration, and positively correlated with the complexity of structures and microtopography. At high elevations, detections were largely confined to boulderfields, and at mid- and low elevations, small mammals were detected primarily in habitats where the subnivean space was most extensive. Antechinus swainsonii and R. fuscipes responded differently to snow cover with the latter seeming better able to overwinter where snow cover was shallow and patchy. In contrast, A. swainsonii occurrence was correlated with the size of the subnivean space. The development of the subnivean space in the Snowy Mountains is dependent on the presence of structures such as shrubs, boulders and microtopographic features that are capable of supporting a snow layer above ground level. The temperature in the subnivean space was virtually constant beneath the snowpack, ranging between 0 and + 1 °C. When snow was patchy or absent, temperatures at ground level were highly variable with a minimum as low s -13°C and maximum as high as +47.5°C. Antechinus swainsonii and R. fuscipes were detected more regularly at sites that were thermally variable. At sites with deep and persistent snow cover (maritime snow), subnivean temperatures were stable, but small mammals were detected at low frequencies. At high elevations, boulderfields were favoured by small mammals during the nival period but were no different thermally from other habitats. The limitations imposed by snow cover on small mammals were further verified by a radio tracking study conducted during 2003 at Perisher Creek. That study investigated the home range size and activity patterns of R. fuscipes and A. swainsonii in relation to snow cover. Once continuous snow cover became established, the home range of both species contracted dramatically and there was an increase in home range overlap. Neither species showed any change in diurnal activity patterns. Rattus fascipes showed signs of social interaction during both seasons in contrast to A. swainsonii, which appeared to remain solitary. In winter, R. fuscipes nested communally at a single location, while during autumn the species appeared to use a number of nest sites. There was no significant change in daily activity patterns between autumn and winter in either species. R. fuscipes remained primarily nocturnal during both pre-nival and nival periods while A. swainsonii continued to be active throughout the diel cycle, although there was a slight shift in its peak activity time. Human activities can, have significant effects on the subnivean space and its residents. The physical characteristics of a range of modified snow types were investigated in the vicinity of several ski resorts in Kosciuszko National Park. Human activities associated with snow-based recreation, such as the creation of ski pistes, surface ski lifts and over-snow routes, involve compression of the snowpack and resulted in small or absent subnivean spaces and high snow cover densities compared to unmodified snow cover. To test the effects of the loss of the subnivean space on small mammals, the snowpack was experimentally compressed in high quality subnivean habitats. Detections of R. fascipes and A. swainsonii declined by 75-80%. Burnt sites from the 2002 study were used in 2003 to investigate the effect of removing vegetation on the subnivean space, to simulate the loss of structure associated with ski slope preparation. There was a significant reduction (p<0.0001) in the size of the subnivean space compared to unburnt sites regardless of habitat type. The key conclusions of the work reported in this thesis are listed below: • Snow conditions in the Australian Alps are markedly different from those of higher northern latitudes and altitudes. As a result, conclusions about snow/fauna interactions based on research in regions with particular snow cover types need to be carefully considered before attempting to extrapolate generalisations to other parts of the world. • The subnivean space can be formed either by passive or active processes. The former occurs when there are sufficient competent structures to permit the support of the snow pack above the ground surface, while the latter refers to the ability of small mammals to actively tunnel through relatively low density snow (depth hoar) and thus create their own subnivean space. In Australia the passive process dominates. • The widely held assumption that small mammals are dependent on the thermally stable conditions in the subnivean space was not confirmed. Rattus fascipes and A. swainsonii survive in the Australian Alps because they are able to exploit thermally variable environments. • Management of human activities in nival areas should focus on avoiding disturbance in areas where a subnivean space forms, particularly in high quality winter habitats such as boulderfields. • Global warming resulting from climate change is likely to provide conditions in the Australian Alps that favour an expansion of the distribution and population of R. fuscipes and A. swainsonii, but nival endemics such as Burramys parvus and possibly Mastacomys fuscus may be at a disadvantage. • The extent of alpine and subalpine environments in Australia will decrease in future, imposing greater pressure on a shrinking resource and raising the possibility of conflict between user groups and conservation imperatives.

Reports of interactions between marine mammals and fisheries are on the increase globally. This is mainly because fishery effort has increased to feed the burgeoning human population and because advances in technology have allowed fisheries to exploit habitats that were until recently inaccessible. Additionally, many marine mammal populations decimated by harvesting over the past few hundred years are recovering and the growing conservation community is paying unprecedented attention to their welfare and conservation generally, with growing interest in their interactions with fisheries. Operational interactions are conspicuous and involve the close contact of marine mammals with fishing gear, either because marine mammals opportunistically or habitually target fishing activities to depredate (i.e. attempt to consume) caught fish, or because marine mammals incidentally encounter fishing gear while foraging naturally. Operational interactions often result in negative outcomes for the conservation and welfare of the marine mammals involved and for the economic viability of the fisheries involved. Marine mammals that become by-caught may receive life threatening injuries from entanglements, or may drown, thus having adverse impacts on small or recovering populations. Fisheries that are targeted by depredating marine mammals may need to replace damaged fishing gear, or may have the catch partially or completely removed, thus having adverse impacts on their economic viability. At the time this body of work commenced, little was being done to address the known or suspected occurrence of operational interactions between marine mammals and several commercial fisheries in the Oceania region. The general aim was to make significant inroads into addressing thesis, by: 1. Reviewing a major fishing method in the two regions in which there are operational interactions with marine mammals; 2. Characterising the nature and extent of depredation and by-catch where operational interactions are known to exist; and 3. Where deemed necessary in those fisheries, developing mitigation strategies and explore their efficacy. Collectively, the five research chapters in this thesis address these aims. They are stand alone case studies of marine mammal depredation and by-catch in commercial fisheries, four of which have already been published in international, peer reviewed journals. The first three research chapters focus on operational interactions involving odontocetes (i.e. toothed whales) and the second two research chapters focus on the otariids (i.e. eared seals). Chapter 2 generally defines and reviews the nature and extend of odontocete (i.e. toothed whale) depredation and by-catch in longline fisheries, which has emerged as an environmental and economic concern internationally. At least 20 odontocete species are involved across all major oceans, although depredation and by-catch rates were variable. This study also introduces fishing gear modification as a viable mitigation strategy. Chapter 3 builds on this theme in more detail by exploring depredation and by-catch, mainly by pilot whales (Globicephala spp.), false killer whales (Pseudorca crassidens) and melon headed whales (Peponocephala electra), in pelagic longline fisheries targeting tuna in Australia and Fiji. Two devices were developed to physically or psychologically deter depredating odontocetes. Unfortunately, the rarity of depredation and by-catch events did not enable the efficacy of the devices to be properly assessed, although both were found to be easily integrated into the normal fishing practice and to have little or no impact on target fish catch rates. Chapter 4 attempts to specifically address the efforts of a purse-seine fishery operating in South Australia (SA) in reducing by-catch of common dolphins (Delphinus delphis), pursuant to conditions set out under the Australian Government Environment Protection Biodiversity Conservation Act 1999 (EPBC Act). After characterising the nature and extent of the problem, it was found that a combination of a Code of Practice (CoP) using avoidance and release strategies and of gear modifications resulted in a reduction in encirclement by-catch from an estimated 377 to eight mortalities each year. Chapters 5 and 6 attempt to assess the impact of a demersal gill-net fishery on the Endangered Australian sea lion (Neophoca cinerea) in waters adjacent to SA. Specifically, Chapter 5 assesses the performance of the Great Australian Bight Marine Park (GABMP) in protecting animals of populations residing within it, pursuant to a management plan that aims to uphold the spirit of the EPBC Act. It was found that individuals tracked using satellite transmitters spent only 27.7% of their time inside the GABMP and could travel up to 9 times further than the location of the southern boundary. Additionally, it was found that by-catch occurred beyond the southern boundary and also within the GABMP during the six months each year that the fishery was allowed to operate within it, with an estimated 14 to 33 individuals killed each 17.6 month breeding cycle. Based on these findings, Improvements to the GABMP were recommended. In a similar manner to chapter 4, chapter 6 directly addresses recommendations pursuant to the EPBC Act to quantify the impact of a demersal gill-netting on all Australian sea lions across SA, by quantifying the extent of geographic overlap and the level of by-catch mortality and extent of overlap between the two. It was found that the two overlapped extensively in 68.7% of 4 km-2 cells and that by-catch was high, at 283 to 333 killed each breeding cycle. Based on these results, it was suggested that a network of permanent and temporary closures along with more extensive monitoring of fishing activities be considered. In summary, this thesis demonstrates that with sufficient political will, stakeholder support and the necessary funds, by-catch and depredation issues can be addressed and can lead to favourable outcomes for the marine mammal populations and commercial fisheries involved. Each case study presented provides many lessons, some being specific to the operational interaction, the marine mammal species or the fishery, and some being more generally applicable. Regarding the latter, more general lessons, it is acknowledged that depredation and by-catch are statistically rare events that may vary across time and space. As such, investigating and addressing them is likely to be costly, with the results still only providing a snapshot or a broad estimate that may not be representative of the overall problem. Additionally, marine mammals are intelligent and may quickly learn how to circumvent mitigation measures, despite their complexity and cost. Although marine protected areas (MPAs) such as the GABMP are implemented with the best intentions, they are often of insufficient size to provide adequate protection and may also allow a level of fishing that still has a quantifiable impact. Despite these drawbacks, all stakeholders are encouraged to adopt a spirit of collaboration and of commitment to attempting to resolve operational interactions with marine mammals where possible. Acoustic deterrence devices have many problems that are yet to be resolved, including their impractically large size and limited sound propagation and battery life. Nonetheless, their amalgamation with some of the physical deterrence technologies developed in chapter 3 may provide a more generic method of deterrence across all fisheries, thus providing hope that resolving operational interactions between marine mammals and commercial fisheries may be a viable proposition in the future.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2013

The earth is currently believed to be in the midst of a mass-extinction episode. Globally, approximately a quarter of mammal species are at risk of extinction. To prevent further degradation of mammals, it is important to understand what causes species to decline, and why some species seem to be more vulnerable than others. Comparative studies in vertebrate taxa often find that a small geographic range size is a strong predictor of high extinction risk. I found that current range size in Australian mainland mammals is a response to previous threatening processes. Using current range size as a predictor of extinction risk is therefore circular. Models that include current range size also tend to underestimate levels of latent extinction risk (the discrepancy between a species' current extinction risk and that predicted from its biological traits), giving misleading predictions of the species and regions with greatest potential for future species declines. Torpor has been associated with both raised and lowered extinction risk due to factors related to energetic efficiency and predation. I found that undertaking torpor reduces extinction risk in mammals, both overall, and specifically in groups threatened by predation. Understanding causes of extinction on islands is critical as islands host endemic species and are refuges for many species now extinct on continents. I found that island mammal extinctions result from complex interactions of introduced predators, island geography, and prey biology. Most notably, extinction probabilities are lower on islands with both black rats and a larger introduced predator (cats, red foxes or dingoes), compared to islands with rats but no larger predator. One conservation implication of this is that eradication of introduced apex predators from islands could precipitate the expansion of black rat populations, potentially leading to extinction of native mammal populations. Conservation now aims to preserve evolutionary history as well as species richness. Using a range of extinction scenarios, I modelled possible future phylogenetic diversity loss on Australia's islands. Under all scenarios, islands in the east of the Bass Strait and the north-east of Northern Territory seem to be centres of phylogenetic diversity loss. As such, we recommend that these islands be prioritised for conservation consideration. Body size is recognised as an important driver of extinction risk, with larger species being at higher risk globally. However, in Australia, it has been argued that ""critical weight range"" mammals (those between 35 and 5500g) are the most vulnerable to decline due to being the preferred prey size for the introduced predators, cats and red foxes. I examined whether Australia's islands tend to have extinctions clustered around a body size significantly smaller or larger than expected by random, and discovered that approximately equal numbers of islands have significantly larger and smaller sized extinctions than expected. Significantly smaller sized extinction clusters predominantly occur in the southeast of Australia. Extinctions on islands with larger introduced predators tend to be biased towards mid-sized species, supporting the theory that foxes and cats can drive size-biased extinctions.

The Australian arid zone has the highest recent mammal extinction rate in the world with most species in the critical weight range of 35 g to 5.5 kg now regionally or globally extinct. Reversing arid zone mammal decline has become a major focus for conservation organizations and reintroduction programs are a common tool in species recovery. Unfortunately, reintroduction success in Australia is low and predation from introduced cats and foxes is commonly cited as the cause of reintroduction failure. In this thesis, I aimed to improve reintroduction success in the arid zone by exploring predation, release protocols and post release abundance at the Arid Recovery Reserve in northern South Australia. Firstly, I attempted to reintroduce threatened mammal species into both a predator free area and one where predators were controlled. Results suggested that successful reintroductions only occurred when cats and foxes were excluded. I then tested different predator reduction strategies to determine if reintroduction success could be improved, including aerial baiting, strategic bait placement and the use of a native top-order predator. Although the use of dingoes to control foxes and cats showed promise, I was unable to improve reintroduction success using poison baiting as it did not significantly reduce feral cat abundance. I investigated the role of release strategies on reintroduction success and conducted predator avoidance training, soft and hard releases and using captive versus wild stock. Predator avoidance training did not assist long term reintroduction success of the bilby but some behavioural differences were detected. Results suggest that Australian arid zone species may be able to learn predator avoidance behavior but this may not necessarily translate into improved reintroduction outcomes. The use of soft and hard releases and captive and wild stock had little effect on reintroduction success when cats and foxes were excluded. Interspecific differences in post-release mortality and behaviour indicated that soft releases may be useful at unrestricted release sites, in situations of high predation risk and where social, sedentary species which invest heavily in their shelters are being released. Finally, I analysed long term monitoring data for four reintroduced threatened species to determine whether factors such as rainfall, time since release or temperature influenced postrelease population fluctuations. Factors significantly influencing abundance included the Indian Ocean Dipole and temperature. Time since release was still the most important factor influencing abundance even 10 years after release indicating that reintroduced populations may not stabilize for decades and long term monitoring is essential. Regardless of reintroduction protocols, new methods of broadscale cat control are required before broadscale reintroduction success can be improved in the Australian arid zone. Present control methods are insufficient to enable successful reintroductions of cat-sensitive mammal species without exclusion fencing. However, exclosures are relatively small and expensive, and can create problems such as overstocking. Future arid zone reintroductions should focus on broadscale reintroductions without fences to ensure widespread recovery but this will require the development of improved cat control methods. Species-specific predator thresholds are also needed to trigger management actions and improve the predictability of reintroduction outcomes.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2012

Marsupials have complex and interesting socioecology and life history strategies that differ quite markedly to much - studied eutherian mammals. However, the socioecology and life history strategies of a number of Australian marsupials are most often observed only within the context of a much larger study on their ecology. My aim was to study, using a combination of behavioural observations and molecular DNA techniques, aspects of the socioecology of a population of yellow - bellied gliders ( Petaurus australis ) in Rennick State Forest, south - western Victoria. Petaurid gliders feed on plant and insect exudates, pollen / nectar and arthropods. Yellow - bellied gliders are arboreal, rare, nocturnal and cryptic, have persistent pair bonds, are territorial and exist in low population densities. In particular, I sought to confirm that the Rennick population of yellow - bellied gliders maintained a predominantly monogamous mating system. I also sought to confirm that the timing of reproduction in this population of yellow - bellied gliders would be seasonal, and timed to coincide with peaks in the abundances of two indices of protein food resources ( i.e. flowering and bark shed ). In a more broadscale study, I sought to examine the geographic distribution of mitochondrial haplotyes and morphological variation of the yellowbellied glider throughout its range. Polymorphic microsatellite loci are the choice of genetic marker for fine - scale studies, such as relatedness and paternity. Microsatellite loci had previously only been characterised and optimised for Petaurus norfolcensis ( squirrel gliders ). However, close inspection of the GenBank sequences revealed the presence of replicates differing only by sequencing errors. A panel of seven polymorphic tetranucleotide loci in Petaurus breviceps ( sugar gliders ) and three polymorphic trinucleotide loci in P. australis were isolated and optimised. Five P. breviceps loci were polymorphic in P. norfolcensis and two were polymorphic in P. australis. Only one P. australis locus was variable in P. breviceps and P. norfolcensis. No locus showed a deficit in heterozygotes according to Hardy - Weinberg expectations, and the large number of alleles for some of the loci confirmed their usefulness for studies in relatedness and paternity. A number of Australian arboreal marsupials have been reported to show monogamous and polygynous mating systems in different populations, but previous studies have not included genetic analyses to confirm the observations. My aim was to test the hypothesis that monogamy was the predominant mating system in a population of yellow - bellied gliders ( Petaurus australis ) in south - western Victoria. Home range overlap, cohesiveness of pairs, rates of den site co - occupancy and location of den trees within the home ranges of 13 gliders were determined via radio - tracking. A monogamous social system predominated, demonstrated by extensive home range overlap between cohabiting adult males and females ( 40 - 100 % ) and little home range overlap between adjacent territories ( < 7 % ). Males spent approximately 55 % of their active time within 25m of their female partners and 55 - 85 % of their sleeping time in dens with their female partner. The paternity of all juveniles within the population was analysed using five microsatellite DNA markers. Of 37 individuals genotyped, 12 of 13 juveniles could be attributed to the resident adult male. My results suggest that social monogamy equates with genetic monogamy in this population of yellow - bellied gliders. Mammalian taxa living in seasonal environments usually coincide energy - demanding reproductive activities with the seasonal availability of food resources. However, few studies on arboreal marsupial taxa in Australia have focussed upon the interplay of forest phenology and the timing of breeding. This study examined forest phenology in a temperate environment, and the timing of reproduction the yellow - bellied glider. I captured adult females once per month between August 2001 and August 2003 to determine reproductive condition, and monitored indicators for two key food resources over the same period. Flowering phenology ( as an index of pollen availability ) was assessed in 170 manna gum ( Eucalyptus viminalis ) and brown stringybark ( E. baxteri ) trees, while bark shed ( as an index of arthropod availability ) was assessed in 45 manna gum, the only eucalypt species at this site that sheds it bark. Aseasonal reproduction was indicated within this population of gliders, as distributions of births were not statistically different from random. However, yellow - bellied gliders did exhibit distinct birth peaks in spring, summer and winter, when data were combined for both years. The temporal distributions of flowering for both eucalypt species were statistically different from random, indicating seasonal availability of nectar and pollen. Peak flowering occurred in summer for brown stringybark, and autumn for manna gum in both years, although for manna gum peak abundance of flowers was one month earlier in the second year. While the temporal distribution of bark shed on the trunks of trees did not differ from random, it did show seasonality on the main and outer branches, peaking in summer and declining thereafter. Thus, it appears that yellow - bellied gliders breed aseasonally in a predictable, seasonal environment. However, yellow - bellied gliders have a reliance on the complex temporal interplay of different seasonal food resources. Subspecific status has often been used as a surrogate for conservation unit, but does not always reflect intra - specific lineages with different evolutionary histories. One contentious case of subspecific classification occurs in the yellow - bellied glider, a marsupial species showing considerable decline in population size and requiring conservation management. Our aim was to assess the current subspecific status of populations and define units of conservation using a combination of phylogeographical analyses of mitochondrial DNA and morphological analyses. Analyses of the mitochondrial ND4 gene provided evidence for significant phylogeographic structure within yellow - bellied gliders. Isolated populations in north Queensland ( NQ ) and Victoria / South Australia were genetically distinct from populations in New South Wales and southern Queensland. Morphological analyses provided little evidence for discrimination of populations, although NQ specimens were generally smaller in size compared to southern forms. My analyses do not support the classification of subspecies, P. a. reginae, for the original type specimen from southern Queensland. Taking into account other behavioural and ecological data, and the disjunct distribution of NQ populations from southern populations, I propose that the NQ population represents a distinct Evolutionarily Significant Unit, a lineage showing highly restricted gene flow with the rest of the species.
http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1281000
Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2006.

This thesis documents the history of Quaternary mammalian faunas from the northern Monaro region of the southern highlands of Eastern Australia. The area currently has a cold semi-arid climate and, together with a series of fossil localities of different ages, provides an opportunity to examine the relationships between faunal changes and palaeoenvironments in this part of Australia during the Quaternary. Fossil material from seven localities within the northern Monaro region is described together with the geology of the sites in which they occur. The localities are Pilot Creek, Bunyan Siding, South Bunyan, Bulong, Tannery Creek, Ryries Creek and Rock Flat Creek, all on tributaries of the Murrumbidgee River near Cooma. Detailed stratigraphic studies, incorporating several dating techniques have been employed at the two major fossiliferous deposits, Pilot Creek and Bunyan Siding. A stratigraphic sequence 1s proposed in which the contained faunas are ordered chronologically. The oldest dated mammal fossil-bearing deposit in the region is at Bunyan Siding. It is an alluvial deposit and comprises two fossiliferous Quaternary units, which disconformably overlie Miocene palaeolake sediments of the Bunyan Formation. The Quaternary units are described as two new formations, the Jilliby Folmation and Nestle Brae Formation. They are interpreted as having been formed in a fluvial environment consisting of large and small meandering channels and adjacent floodplains. Dating of the site using palaeomagnetism and optically stimulated luminescence establishes a Middle Pleistocene age (120- 780 ka) for both units. Two local faunas are recognised at Bunyan Siding, the Jilliby Local Fauna and Nestle Brae Local Fauna, each defined and named after the stratigraphic units that contain them. The other major locality, Pilot Creek, is a valley-fill sequence comprising a series of channel cut-and:-fill units and marginal alluvial fans of Late Pleistocene and Holocene ages. Five stratigraphic units are recognised and described in detail including the description of two formations, Pilot Creek and Willow Bank. Each unit contains a local fauna. Fourteen radiocarbon dates enable absolute ages to be placed on some of the units. The oldest fossiliferous unit in the Pilot Creek sequence is the Pilot Creek Formation which has been radiometrically dated at circa 25 ka years BP. The next youngest unit in the sequence is an alluvial fan deposits, QF1 which has been dated at 11 ka. A third unit, the Willow Bank Formation, is a channel-fill unit which truncates both the Pilot Creek Formation and the QF1 unit. Dates from the Willow Bank Formation range from 6 ka to 2 ka. A second alluvial fan unit, QF2 inset into the Pilot Creek Formation, is dated at 4.5 ka. A recent alluvial unit, PESA, is at the top of the sequence. From the stratigraphy of th~ valley units five local faunas have been defined, providing a faunal record in the valley spanning the last 25 ka.

In Port Phillip Bay, Victoria, Australia, the endemic and vulnerable Burrunan dolphin (Tursiops australis) is the target species of a non-consumptive, economically important, dolphin-swim industry. This industry commenced in 1986, and southern Port Phillip Bay is now a key eco-tourism destination in Victoria, with 8 permitted trips daily targeting swimming with Burrunan dolphins. Although this industry has been in operation for 29 years, understanding of the occurrence, demographics, habitat use, behaviour and effects of tourism on Burrunan dolphins is limited. This lack of empirical data is of concern as it has impeded management of the Port Phillip Bay dolphin-swim industry. To ensure the sustainability of this industry, it is imperative that sound scientific data be provided so that management can make informed decisions. This study assessed the potential effects of the dolphin-swim industry on Burrunan dolphin behaviour whilst simultaneously assessing the efficacy of different management strategies.

Otariid seals pose several challenges in collecting behavioural data due because of the geographical decoupling of breeding habitat (terrestrial) and foraging grounds (aquatic). Additionally, life history traits such as breeding chronology and moult state constrain the temporal window over which data can be collected. Expensive telemetry devices coupled with logistical difficulties and the biology of animals often limits the ability to answer questions concerning the role of seasonal or life-history differences in foraging ecology. However, quantifying individual behavioural specialisations such as foraging behaviour that may impede gene flow is an essential prerequisite to understanding population structure. Several unusual life history traits of the IUCN Red Listed (threatened) Australian sea lion Neophoca cinerea are interesting from an ecological, evolutionary and conservation standpoint. Australian sea lions are endemic to the southern and western coastline of Australia, distributed over approximately 70 breeding colonies with 86% of all breeding occurring in South Australia. Most notably, a unique 17.5month breeding chronology and asynchronous breeding between spatially-close colonies has been proposed to be an adaptive response to a low-quality foraging environment that has little or no seasonality. Contrary to this, recent studies suggest at least the South Australian range of the species is a region replete with mesoscale areas of seasonally rich productivity, further supported by the presence of large numbers of other top marine predators and the largest volume fishery in Australia. In the face of this contradiction, the ecological determinants of population structure clearly have yet to be identified. To address these key knowledge gaps, this study explored the population structure and foraging behaviour of adult female Australian sea lions at seventeen of the largest breeding colonies across the South Australian range. A novel screening technique which employed δ¹³C and δ¹⁵N present in the whiskers of wholly milk-dependent pups was developed and validated as a proxy for maternal values. Mother-to-pup fractionation was quantified, with a δ¹⁵N enrichment of +1.92‰ (blood) and +1.27‰ (vibrissae). Subsequent large-scale sampling of >50% of all pups born on each colony suggested a degree of ecological partitioning over a spatial scale never previously described for otariids. Isotope ratios of serially-subsampled vibrissae from 20 adult female Australian sea lions across seven breeding colonies revealed individual long-term temporal consistency in both foraging site (offshore vs inshore) and prey selection. Furthermore, dive and movement parameters did not differ between alternate foraging ecotypes, suggesting that the alternate foraging strategies of adult female Australian sea lions were temporally persistent and unrelated to phenotypic variation. Finally, individual foraging specialisation and matrilineal population structure were integrated by obtaining isotope and mitochondrial DNA (mtDNA) samples from over 50% of all pups born at each of 17 breeding colonies in order to characterise foraging ecotype composition and matrilineal population structure. Alternate foraging ecotypes were present at almost every colony with no evidence to support particular mitochondrial lineages were restricted to specific foraging ecotypes. Spatial analysis of molecular data identified three putatitive clusters of colonies that share multiple haplotypes being interspersed with 9 singleton breeding sites, with genetic structure becoming more apparent at colonies closer to deep water. Colonies with little or no similarity in mtDNA haplotype composition were more likely to breed asynchronously irrespective of the geographic distance between them. Contrary to expectations, the propensity for individual animals to forage offshore was unrelated to the proximity of breeding colonies to deep water. This study adds considerable knowledge to our current understanding of Australian sea lion foraging behaviour and highlights the inappropriateness of making broad-scale inferences about foraging ecology or population structure in this species. Individual foraging specialisation may act as an ecological barrier to migration, with individuals only able to disperse to colonies within range of preferred fine-scale foraging habitat where they have appropriate hunting skills.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2012

Australia has one of the world's worst rates of mammal extinctions, accounting for about one third of the mammal species that have become extinct in the world since 1600 (Burbidge and Manly 2002). Most of these documented declines and extinctions have been concentrated towards mammals in the arid-zone of central Australia. In South Australia (SA), one of the arid-zone species that has undergone substantial declines in range and abundance is the black-footed rock-wallaby, Petrogale lateralis (MacDonnell Ranges race). Animals are now restricted to the Anangu Pitjantjatjara Yankunytjatjara (APY) Lands in the state's far north-west, where there remain two known metapopulations. The decline of this race, which is known as 'warru' by Western Desert Indigenous people, is presumed to have been precipitated by introduced predators. However, in order to exclude other potential causes and establish if recovery is feasible, the current project investigated the ecology of warru in the SA APY Lands. In order to make inferences about the habitat and environmental conditions that best facilitate warru persistence, a modelling approach at multiple spatial scales was used. At a landscape scale, warru presence was correlated to geology, slope, soil type and elevation. At a finer scale, fieldwork established that a number of parameters, including aspect, vegetation, rock complexity and refuges' physical characteristics were important determinants of warru presence and use. The work presents the first analysis of P. lateralis habitat requirements. To establish animals' use of this preferred habitat, the thesis provides preliminary data on warru home range and movement patterns. Unfortunately, catastrophic failure of Global Positioning System collars meant that data were limited to those from one adult female in one month. Nevertheless, during this time, the animal had a larger than expected home range and undertook a number of long-range movements, including a sojourn off the hill. These results have implications for management, including predator and fire management strategies. An investigation of the genetic structure of animals in the three largest-known warru colonies indicated that all colonies are genetically diverse, with levels of heterozygosity approximating expected values. All three also exhibited substantial population structuring, with genetic groups correlating to geographic colonies. However, there was also evidence for sub-structuring being present within one of the colonies and for migration occurring into two colonies, with approximately 5% of sampled individuals having mixed ancestry. An analysis of the parentage of offspring indicated that warru have a polygamous mating structure, although one instance of intra- and inter-year monogamy was also established. Population modelling was used to provide an estimate of the sizes of each of the three studied colonies. Combined with recent aerial survey data, these data suggested that there are likely to be fewer than 200 warru remaining in SA. However, all three colonies showed signs conducive to potential recovery, including high average reproductive rates, even sex ratios and high adult survivorship (>75%). Juvenile survival, however, was significantly lower (51%) and positively correlated with winter rainfall, indicating that access to water is important during the drier winter months. The potential for warru recovery was supported by an analysis of warru blood chemistry in both the wild and captive colonies. The latter was established as part of the recovery program and aimed to produce animals for in-situ supplementation and reintroduction. In 2009, when blood samples were taken, warru colonies did not manifest with results that are indicative of population-wide disease. However, the biochemical parameters of animals in one of the in-situ colonies, 'New Well', suggested some level of nutritional and water stress. This suggests that managers could consider providing warru at New Well with supplementary food and water during drought, and/or using fire to promote vegetational diversity. The study presents the first detailed haematological reference values for P. lateralis and potentially, a methodology for other threatened species recovery programs to follow in order to establish the health of their populations. The current results have implications for management of both the in- and ex-situ warru populations. For example, results pertaining to habitat selection can be used to guide selection of appropriate reintroduction sites. Overall, results indicate that although the extant colonies have small population sizes, the animals therein have high reproductive rates, are not suffering the effects of disease and are genetically diverse. The rock-wallabies' polygamous mating strategy is also likely to continue to facilitate this genetic diversity. Furthermore, although warru have specific habitat preferences, they have the capacity to disperse to surrounding available habitat. Overall, this suggests that, given appropriate management, warru recovery is feasible. Some of these data may also be pertinent for management of P. lateralis in the Northern Territory and Western Australia.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2011