Based on the recommendations of both the 1993 Reintroduction biology of Australasian Fauna Conference and the 1994 Rock Wallaby Symposium, captive-bred Yellow footed rock wallabies were reintroduced into areas of their former ranges in both South Australia and Queensland

Conservation biology is primarily concerned with the amelioration of species decline. The Yellow-footed Rock-wallaby (Petrogale xanthopus xanthopus) is a medium-sized Macropod that inhabits the semiarid rangelands of South Australia and New South Wales. Its conservation status is Vulnerable C2a(i). In this study, population modelling, spatially explicit habitat modelling and Population Viability Analysis (PVA) have been used to better understand the factors that affect the abundance and distribution of the P. x. xanthopus in South Australia. The processes that drive the population dynamics of a species operate at different scales. As such this research involves a collection of several inter-related and scale-specific empirical studies that provide insights about the population dynamics of P. x. xanthopus. Each of these studies captures environmental, demographic and behavioural process acting on the population at different scales. These include the analysis of relative abundance data derived from an aerial census, mark recapture sampling of demographic parameters in relation to rainfall patterns and a collection of habitat models derived at different scales using presence-absence data. Spatially explicit PVAs enable the population dynamics of a species to be modelled in space and time. Using these data, a PVA is conducted to explore and rank the importance of the factors that threaten this species and help guide their future monitoring and management. Movement is also a key issue when considering problems such as isolation and inbreeding. Given that little is known about the dispersal behaviour of this species, a range of different dispersal behaviours are also simulated in the PVA using random and non-random mating algorithms, to estimate the potential for inbreeding. / thesis (PhD)--University of South Australia, 2004.

Microsatellites are simple repetitive DNA sequences that are used as genetic markers throughout the biological sciences. The high levels of variation observed at microsatellite loci contribute to their utility in studies at the population and individual levels. This variation is a consequence of mutations that change the length of microsatellite repeat tracts. Current understanding suggests that most mutations are caused by polymerase slippage during DNA replication and lead to changes of a single repeat unit in length, but some changes involving multiple repeats can also occur. Despite this simplistic overview, there is evidence for considerable heterogeneity in mutation processes between species, loci and alleles. Such complex patterns suggest that other mechanisms, including those associated with DNA recombination, are also involved in the generation of microsatellite mutations. Understanding which mutational mechanisms are responsible for variation at microsatellite markers is essential to enable accurate data interpretation in genotyping projects, as many commonly used statistics assume specific mutation models. I developed microsatellite markers specific to the X and Y chromosomes and an autosome in the tammar wallaby, Macropus eugenii, and investigated their evolutionary properties using two approaches: indirectly, as inferred from population data, and directly, from observation of mutation events. First, I found that allelic richness increased with repeat length and that two popular mutation models, the stepwise mutation model and the infinite allele model, were poor at predicting the number of alleles per locus, particularly when gene diversity was high. These results suggest that neither model can account for all mutations at tammar wallaby microsatellites and hint at the involvement of more complex mechanisms than replication slippage. I also determined levels of variation at each locus in two tammar wallaby populations. I found that allelic richness was highest for chromosome 2, intermediate for the X chromosome and lowest for the Y chromosome in both populations. Thus, allelic richness varied between chromosomes in the manner predicted by their relative exposure to recombination, although these results may also be explained by the relative effective population sizes of the chromosomes studied. Second, I used small-pool PCR from sperm DNA to observe de novo mutation events at three of the most polymorphic autosomal markers. To determine the reliability of my observations I developed and applied strict criteria for scoring alleles and mutations at microsatellite loci. I observed mutations at all three markers, with rate variation between loci. Single step mutations could not be distinguished because of the limitations of the approach, but 24 multi-step mutations, involving changes of up to 35 repeat units, were recorded. Many of these mutations involved changes that could not be explained by the gain or loss of whole repeat units. These results imply that a large number of mutations at tammar wallaby microsatellites are caused by mechanisms other than replication slippage and are consistent with a role for recombination in the mutation process. Taken as a whole, my results provide evidence for complex mutation processes at tammar wallaby microsatellites. I conclude that careful characterisation of microsatellite mutation properties should be conducted on a case-by-case basis to determine the most appropriate mutation models and analysis tools for each locus. In addition, my work has provided a set of chromosome-specific markers for use in macropod genetic studies, which includes the first marsupial Y chromosome microsatellites. Sex chromosome microsatellites open a new range of possibilities for population studies, as they provide opportunities to investigate gene flow in a male context, to complement data from autosomal and maternally-inherited mitochondrial markers.

Reductive acetogenesis via the acetyl-CoA pathway is a hydrogenotrophic pathway that has the potential to reduce methanogenesis from ruminant livestock. However our understanding of the organisms capable of this transformation (acetogens) is hindered by a lack of specific molecular tools for this group. In the present thesis, a PCR primer set specific for a wide range of acetogens was developed, targeting the acetyl-CoA synthase (ACS) gene which is unique to the acetyl-CoA pathway. ACS was found to be useful marker for potential acetogens and ACS sequences could be used to infer family-level phylogeny for many acetogens. ACS gene specific primers were used in combination with existing molecular tools targeting the gene encoding formyltetrahydrofolate synthetase (FTHFS, present in the acetyl-CoA pathway but not unique to it) and 16S rRNA genes, as well as cultivation techniques, to investigate acetogen diversity in the rumen and two analogous gut systems where microbial hydrogenotrophy differs: the forestomach of a native Australian marsupial, the tammar wallaby Macropus eugenii; and the developing rumen of young lambs. Novel potential acetogens present naturally in the rumen of pasture fed and grain fed cattle affiliated with the Ruminococcaceae/Blautia group and distantly with the Lachnospiraceae. A large diversity of potential acetogens with functional genes affiliating broadly between the Lachnospiraceae and Clostridiaceae though without a close sequence from a cultured relative were also detected. Rumen acetogen enrichment cultures revealed the presence of a known acetogen, Eubacterium limosum, in grain fed cattle, as well as novel acetogens affiliating with the Lachnospiraceae and Ruminococcaceae/Blautia group. The novel potential acetogen population detected in this study may represent an important hydrogenotrophic group in the rumen that we understand very little about and that requires further investigation. The tammar wallaby, which exhibits foregut fermentation analogous to that of the rumen but resulting in lower methane emissions, housed a different acetogen population to that of the bovine rumen (LIBSHUFF, p <0.0001) though novel potential acetogens in the tammar wallaby forestomach affiliated broadly in the same family groups (Blautia group, Lachnospiraceae and between Lachnospiraceae and Clostridiaceae without a close cultured isolate). Acetogen enrichment cultures from the tammar wallaby forestomach facilitated isolation of a novel acetogen, which was closely related to potent reductive acetogens from kangaroos. The differences between the acetogen population of the tammar wallaby forestomach and the bovine rumen may be a factor in explaining lower methane emissions and methanogen numbers in tammar wallabies relative to ruminants. Using a gnotobiotically reared lamb model, the unique acetogen population present in the developing rumen was identified and it’s response to methanogen colonisation examined. The acetogen E. limosum and potential acetogen Ruminococcus obeum were identified as well as a small diversity of novel potential acetogens affiliating with the Blautia group and the Lachnospiraceae. A small but diverse population of naturally resident methanogens were also identified in gnotobiotically reared lambs that had been isolated at 17 hours of age. After inoculation with Methanobrevibacter sp. 87.7, methanogen numbers in gnotobiotically reared lambs significantly increased but acetogen diversity was not altered, indicating that this population is resilient to methanogen colonisation to some degree. The potential acetogen population in gnotobiotically reared lambs was significantly different (LIBSHUFF, p < 0.0001) to that in conventionally reared sheep, which indicates that factors other than methanogen establishment alone, probably relating to other microbes and associated hydrogen concentrations in the rumen, affect acetogens during rumen development.

Conservation biology is primarily concerned with the amelioration of species decline. The Yellow-footed Rock-wallaby (Petrogale xanthopus xanthopus) is a medium-sized Macropod that inhabits the semiarid rangelands of South Australia and New South Wales. Its conservation status is Vulnerable C2a(i). In this study, population modelling, spatially explicit habitat modelling and Population Viability Analysis (PVA) have been used to better understand the factors that affect the abundance and distribution of the P. x. xanthopus in South Australia. The processes that drive the population dynamics of a species operate at different scales. As such this research involves a collection of several inter-related and scale-specific empirical studies that provide insights about the population dynamics of P. x. xanthopus. Each of these studies captures environmental, demographic and behavioural process acting on the population at different scales. These include the analysis of relative abundance data derived from an aerial census, mark recapture sampling of demographic parameters in relation to rainfall patterns and a collection of habitat models derived at different scales using presence-absence data. Spatially explicit PVAs enable the population dynamics of a species to be modelled in space and time. Using these data, a PVA is conducted to explore and rank the importance of the factors that threaten this species and help guide their future monitoring and management. Movement is also a key issue when considering problems such as isolation and inbreeding. Given that little is known about the dispersal behaviour of this species, a range of different dispersal behaviours are also simulated in the PVA using random and non-random mating algorithms, to estimate the potential for inbreeding. / thesis (PhD)--University of South Australia, 2004.

This study aimed to determine whether rainfall regime has driven differentiation in the Australian perennial grass, Austrodanthonia caespitosa, resulting in local ecotypes possessing characters, such as deep rootedness or summer activity, that may be particularly useful in reducing deep drainage for salinity mitigation, or whether the species shows a plastic response in root growth to soil water distribution. Rainfall regime varies within a given annual rainfall because size and ditribution of rainfall event vary. This can have an important effect on soil water distribution, both spatially and temporally. This study investigates the relationship between rainfall regime and the structure of root systems in local populations of Austrodanthonia caespitosa (Gaudich.), Firstly, it examined a number of indices useful in quantifying variation in small-scale rainfall regime, including seasonal bias, event size, event frequency, and the clustering of events, as well as how rainfall event size may be changing over time across Australia. The variation in soil water distribution that results from different rainfall regimes is expected to interact with root distribution in plants, either acting as a selective force and driving genotypic differentiation in response to soil water availability, or through plasticity in root placement. The relationship between rainfall regime and root depth distribution was examined in Austrodanthonia caespitosa (Gaudich.), or white-top wallaby grass, a perennial grass common across southern Australia. Growth and reproductive traits of plants grown from seeds collected from across the range of this species under a single rainfall regime were compared and correlated with the rainfall indices and soil type in order to establish possible abiotic explanations for trait variability. Phenological characters were found to be particularly variable between ecotypes, but high local variation between ecotypes suggested factors operating on a spatial scale smaller than the rainfall gradients are responsible for population differentiation. In order to investigate the interaction between rainfall event size and root depth, an experiment was conducted to investigate plant response to watering pulse size and frequency, with plants grown under a range of controlled watering regimes, and root depth distribution compared. The primary response in root growth was plastic, with shallow roots being developed under small, frequent events, and deep roots developed under large, infrequent waterings. Differences between ecotypes were less important, and there was no interaction between ecotype and watering treatment, indicating the same degree of plasticity in all ecotypes. Plants from a range of populations were grown under a controlled climate, first under winter conditions, then under summer conditions, with summer water withheld from half the plants, in order to determine the response to summer watering and summer drought. Plants that were watered over summer showed a strong growth response, increasing shoot biomass significantly. This effect was particularly strong in South Australian populations, which was unexpected as they originate from a region with low, unpredictable summer rainfall. Root depth was not strongly influenced by summer watering treatment. Finally, an evolutionary algorithm model was constructed in order to examine optimal plant traits under a variety of rainfall regimes. The model highlighted the importance of the interaction between rainfall regime and soil type in determining optimal root placement. Variable root cost with depth was also found to be an important trade-off to be considered, with high root loss in the surface soil layers, due to high temperatures, making a shallow rooted strategy less efficient than if root costs were equal throughout the root system. Overall, no ecotypes of A.caespitosa could be identified that had characters particularly suited to deep drainage reduction, as the drought tolerant nature of the species, and the dormancy during times of drought, may lead to low overall water use. However, it may be a useful native component in pasture systems, due to its strong growth response to summer rainfall, a characteristic found to be particularly strong in a number of South Australian ecotypes. / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

[Truncated abstract] The Laverton Greenstone Belt (LGB), located in the northeastern part of the Eastern Goldfields Province (EGP) of the Yilgarn Craton, Western Australia, has a total contained gold endowment of over 690t. An important feature of the gold deposits in the LGB is their close spatial association with granitoids, with many gold deposits located adjacent to, or hosted by, granitoids. Recently-proposed genetic models for Archaean orogenic gold deposits have emphasised the role of granitoids in the formation of ore-deposits, but differ significantly in the nature of that role. Some models suggest that the granitoids are a source of ore-fluids and solutes, whereas others suggest that granitoids exert an important structural control on gold mineralisation. Such competing genetic models for gold mineralisation variably propose either a proximal-magmatic or distal-metamorphic, or less commonly distal-magmatic, source for goldbearing fluids, or mixing of fluids from multiple sources. Isotope geochemistry and geochronological studies are used to constrain the source and timing of auriferous fluids at nine gold deposits in the LGB in an attempt to differentiate between conflicting genetic models. To overcome the lack of detailed deposit-scale geological constraints inherent to any regional study, hypotheses generated from regional datasets are tested in a detailed case-study of the Wallaby gold deposit. The Pb-isotope compositions of ore-related sulphides from deposits in the LGB plot along the line representing crustal-Pb in the Norseman-Wiluna Belt of the EGP, with individual deposits clustering with other nearby deposits based on their geographic location. This trend is similar to that recorded in the Kalgoorlie-Norseman region in the southern EGP, and is consistent with a basement Pb reservoir for gold-bearing fluids. As such, data are consistent with a similar fluid source for all gold deposits. The Nd and Sr isotopic composition of goldrelated scheelite in the LGB clusters very tightly. The inferred ore-fluid composition has a slightly positive εNd, similar to ore fluids at other gold deposits in the EGP for which a proximal magmatic source is highly improbable. As such, Sr and Nd data are consistent with a similar fluid source for the gold deposits analysed in the LGB, but cannot unequivocally define that source. The median S, C and O isotopic compositions of ore minerals from all nine different gold deposits studied in the LGB fall in a very narrow range

Bibliography: leaves 107-117. This thesis examines the rationale for managing biological diversity on a regional basis and develops recommendations for the use of two computational methods in biodiversity management planning by conducting a case study in the Flinders Ranges, centred on the Yellow-footed Rock Wallaby (abstract)

[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.

In this thesis a number of statistical methods have been developed and applied to habitat suitability modelling for rare and threatened species. Data available on these species are typically limited. Therefore, developing these models from these data can be problematic and may produce prediction biases. To address these problems there are three aims of this thesis. The _rst aim is to develop and implement frequentist and Bayesian statistical modelling approaches for these types of data. The second aim is develop and implement expert elicitation methods. The third aim is to apply these novel approaches to Australian rare and threatened species case studies with the intention of habitat suitability modelling. The _rst aim is ful_lled by investigating two innovative approaches for habitat suitability modelling and sensitivity analysis of the second approach to priors. The _rst approach is a new multilevel framework developed to model the species distribution at multiple scales and identify excess zeros (absences outside the species range). Applying a statistical modelling approach to the identi_cation of excess zeros has not previously been conducted. The second approach is an extension and application of Bayesian classi_cation trees to modelling the habitat suitability of a threatened species. This is the _rst `real' application of this approach in ecology. Lastly, sensitivity analysis of the priors in Bayesian classi_cation trees are examined for a real case study. Previously, sensitivity analysis of this approach to priors has not been examined. To address the second aim, expert elicitation methods are developed, extended and compared in this thesis. In particular, one elicitation approach is extended from previous research, there is a comparison of three elicitation methods, and one new elicitation approach is proposed. These approaches are illustrated for habitat suitability modelling of a rare species and the opinions of one or two experts are elicited. The _rst approach utilises a simple questionnaire, in which expert opinion is elicited on whether increasing values of a covariate either increases, decreases or does not substantively impact on a response. This approach is extended to express this information as a mixture of three normally distributed prior distributions, which are then combined with available presence/absence data in a logistic regression. This is one of the _rst elicitation approaches within the habitat suitability modelling literature that is appropriate for experts with limited statistical knowledge and can be used to elicit information from single or multiple experts. Three relatively new approaches to eliciting expert knowledge in a form suitable for Bayesian logistic regression are compared, one of which is the questionnaire approach. Included in this comparison of three elicitation methods are a summary of the advantages and disadvantages of these three methods, the results from elicitations and comparison of the prior and posterior distributions. An expert elicitation approach is developed for classi_cation trees, in which the size and structure of the tree is elicited. There have been numerous elicitation approaches proposed for logistic regression, however no approaches have been suggested for classi_cation trees. The last aim of this thesis is addressed in all chapters, since the statistical approaches proposed and extended in this thesis have been applied to real case studies. Two case studies have been examined in this thesis. The _rst is the rare native Australian thistle (Stemmacantha australis), in which the dataset contains a large number of absences distributed over the majority of Queensland, and a small number of presence sites that are only within South-East Queensland. This case study motivated the multilevel modelling framework. The second case study is the threatened Australian brush-tailed rock-wallaby (Petrogale penicillata). The application and sensitivity analysis of Bayesian classi_cation trees, and all expert elicitation approaches investigated in this thesis are applied to this case study. This work has several implications for conservation and management of rare and threatened species. Novel statistical approaches addressing the _rst aim provide extensions to currently existing methods, or propose a new approach, for identi _cation of current and potential habitat. We demonstrate that better model predictions can be achieved using each method, compared to standard techniques. Elicitation approaches addressing the second aim ensure expert knowledge in various forms can be harnessed for habitat modelling, a particular bene_t for rare and threatened species which typically have limited data. Throughout, innovations in statistical methodology are both motivated and illustrated via habitat modelling for two rare and threatened species: the native thistle Stemmacantha australis and the brush-tailed rock wallaby Petrogale penicillata.