Dissertations / Theses on the topic 'Macropus eugenii'

Marsupials and eutherians are the two principal groups of modern mammals. Mammalian immunological studies, to date, have focused on eutherian systems with little or no comprehensive work having been carried out on marsupials. This project investigates the functional and developmental aspects of T-cell responses in the marsupial, Macropus eugenii (Tammar wallaby) in both adults and pouch young at various stages of development. Determination of the age at which the Tammar wallaby immune system becomes competent has been examined through the use of cellular and molecular studies carried out on developing pouch young tissue. The capacity for generating an immunological response in adult and pouch young marsupials has been studied by following cellular proliferation in response to mitogens or mixed lymphocyte culture (MLC). After examining adult responses to mitogens and allogenic lymphocytes, optimised conditions were then used to examine the development of responsiveness in pouch young. Several further tests were conducted and findings shown. The study has shown that the earliest age at which Macropus eugenii is capable of mounting a T-cell mediated immune response is between 5 to 13 days post-partum
Doctor of Philosophy (PhD)

Marsupials and eutherians are the two principal groups of modern mammals. Mammalian immunological studies, to date, have focused on eutherian systems with little or no comprehensive work having been carried out on marsupials. This project investigates the functional and developmental aspects of T-cell responses in the marsupial, Macropus eugenii (Tammar wallaby) in both adults and pouch young at various stages of development. Determination of the age at which the Tammar wallaby immune system becomes competent has been examined through the use of cellular and molecular studies carried out on developing pouch young tissue. The capacity for generating an immunological response in adult and pouch young marsupials has been studied by following cellular proliferation in response to mitogens or mixed lymphocyte culture (MLC). After examining adult responses to mitogens and allogenic lymphocytes, optimised conditions were then used to examine the development of responsiveness in pouch young. Several further tests were conducted and findings shown. The study has shown that the earliest age at which Macropus eugenii is capable of mounting a T-cell mediated immune response is between 5 to 13 days post-partum

"November 2001".
Thesis (PhD)--Macquarie University, Division of Environmental and Life Sciences, Department of Biological Sciences, 2002.
Bibliography: leaves 136-157.
General introduction -- Molecular markers for comparative and quantitative studies in macropods -- Genetic linkage map construction in the tammar wallaby (M. eugenii) -- Intraspecific variation, sex-biased dispersal and phylogeography of the eastern grey kangaroo (M. giganteus) -- General discussion.
The analysis of DNA using molecular techniques is an important tool for studies of evolutionary relationships, population genetics and genome organisation. The use of molecular markers within marsupials is primarily limited by their availability and success of amplification. Within this study, 77 macropodid type II microsatellite loci and two type I genetic markers were characterised within M. eugenii to evaluate polymorphic levels and cross-species amplification artifacts. Results indicated that 65 microsatellite loci amplified a single locus in M. eugenii with 44 exhibiting high levels of variability. The success of crossspecies amplification of microsatellite loci was inversely proportional to the evolutionary distance between the macropod species. It is revealed that the majority of species within the Macropodidae are capable of using many of the available heterologous microsatellites. When comparing the degree of variability between source-species and M. eugenii, most were significantly higher within source species (P < 0.05). These differences were most likely caused by ascertainment bias in microsatellite selection for both length and purity. -- The production of a marsupial genetic linkage map is perhaps one of the most important objectives in marsupial research. This study used a total of 353 informative meioses and 64 genetic markers to construct a framework genetic linkage map for M. eugenii. Nearly all markers (93.7%) formed a significant linkage (LOD > 3.0) with at least one other marker. More than 70% (828 cM) of the genome had been mapped when compared with chiasmata data. Nine linkage groups were identified, with all but one (LG7; X-linked) allocated to the autosomes. Theses groups ranged in size from 15.7 cM to 176.5 cM, and have an average distance of 16.2 cM between adjacent markers. Of the autosomal linkage groups, LG2 and LG3 were assigned to chromosome 1 and LG4 localised to chromosome 3 based on physical localisation of genes. Significant sex-specific distortions towards reduced female recombination rates were revealed in 22% of comparisons. Positive interference was observed within all the linkage groups analysed. When comparing the X-chromosome data to closely related species it is apparent that it is conserved both in synteny and gene order. -- The investigation of population dynamics of eastern grey kangaroos has been limited to a few ecological studies. The present investigation provides analysis of mtDNA and microsatellite data to infer both historical and contemporary patterns of population structuring and dispersal. The average level of genetic variation across sample locations was exceedingly high (h = 0.95, HE = 0.82), and is one of the highest observed for marsupials. Contrary to ecological studies, both genic and genotypic analyses reveal weak genetic structure of populations where high levels of dispersal may be inferred up to 230 km. The movement of individuals was predominantly male-biased (average N,m = 22.61, average N p = 2.73). However, neither sex showed significant isolation by distance. On a continental scale, there was strong genetic differentiation and phylogeographic distinction between southern (TAS, VIC and NSW) and northern (QLD) Australian populations, indicating a current and / or historical restriction of geneflow. In addition, it is evident that northern populations are historically more recent, and were derived from a small number of southern eastern grey kangaroo founders. Phylogenetic comparisons between M. g. giganteus and M. g. tasmaniensis, indicated that the current taxonomic status of these subspecies should be revised as there was a lack of genetic differentiation between the populations sampled.
Mode of access: World Wide Web.
xv, 182 leaves ill

[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.

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.

Thesis (Ph.D.) -- University of Western Sydney, 2002.
"A thesis submitted to the University of Western Sydney in fulfilment of the requirements for the degree of Doctor of Philosophy" Bibliography : leaves 400-437.

The newborn marsupial is born at a highly altricial stage of development when compared to eutherian newborn mammals. Interestingly, the marsupial young are born into a non-sterile environment and lack a developed immune system which prevents them from mounting an adaptive immune response. Two reviews are presented in this thesis. The first review examined the complementary mechanisms which protect the developing marsupial young. Immune protection through forms of innate immunity and maternal contributions has been examined in marsupials. However, as there are many facets to immune protection, our understanding of the protection of the developing marsupial young is far from complete and much of the developing marsupial's innate immune system remains unexplored. Importantly, the review also recognised that the availability of marsupial genomes should be exploited to help direct further research on the protection of marsupial young. The second review examined the role of the pouch in marsupial reproduction. While it is clear that the pouch provides immune protection to those species that have a pouch, the pouch cannot provide immune protection to the young of those species without a pouch. Thus, instead of using the pouch to explain immune protection of marsupial young, the review examined the role of the pouch in supporting highly altricial young and promoting reproductive success in various environments where a pouch may confer significant advantages over free hanging young. The reviews set the direction for the experimental research presented in this thesis. The model species tammar wallaby (Macropus eugenii) was used to further examine innate immune genes. First, innate immune genes, mucin and lysozyme were identified or predicted in the tammar wallaby. The mucin and lysozyme genes were then physically mapped to conserved regions of the tammar wallaby genome which facilitated the confirmation of the identification of the genes. Second, the expression of immune genes was examined in the skin and lung of developing tammar wallabies considered immune-incompetent and immune-competent using transcriptome sequencing. There were 390 and 429 immune genes expressed in developing tammar wallaby skin and lung, respectively, suggesting that both tissues play a role in immune defense. Unexpectedly, mucin and lysozyme were not expressed in the skin and lung of wallabies considered to be immune-incompetent. Further, enrichment analysis of genes identified in Gene Ontology terms showed that specific immune genes, complement component 3, complement factor B and apolipoprotein A1, have increased expression in the skin and lung of wallabies considered immune-incompetent. The increased expression of the immune genes suggests that there may be specific innate immune system processes in play to compensate for the delayed development of the adaptive immune system in marsupial. The research presented in this thesis identified gaps in the research of immune protection of marsupial young and identified, mapped and examined the expression of innate immune genes in the developing tammar wallaby. Thus, we are closer to understanding the complexity of the developing marsupial immune system. The identification of immune genes and their expression, lays the foundation for further functional research in marsupial developmental immunology.

The South Australian mainland tammar wallaby (Macropus eugenii eugenii) was presumed extinct in the wild from the early 1930's, until a feral population was re-discovered in New Zealand. Eighty-five animals were returned to Australia as part of a repatriation program into their former range. The establishment phase after a reintroduction is a critical time as animals may fail to survive if they cannot find resources and avoid predators in an unfamiliar habitat. To maximise reintroduction and establishment success, reintroductions need to be planned with a good understanding of the animals’ ecology and anti-predator strategies. To improve this understanding requires experimental reintroductions and detailed monitoring. This thesis investigates the experimental reintroduction of 46 wallabies into Innes National Park in South Australia and examines the influence of release group familiarity on establishment. Part of this was an investigation of home range, habitat requirements and social behaviours during establishment and seasonally post-establishment. The thesis includes three data chapters which focus on (1) home range and core area, home range stability and degree of overlap with conspecifics; (2) habitat selection at the landscape scale and for day and night use within home range; and (3) factors influencing fine scale habitat use and social grouping behaviours in light of predation risk. In this study, the animals’ perceived risk of predation is assumed to be reflected by surrogate measures of risk, such as distance to cover, likelihood of using cover, group size, and distance to nearest neighbour. Release group familiarity was established by housing animals together in captivity for at least one month prior to release (“familiar” groups), whereas “unfamiliar” release groups comprised animals housed separately but released together. After each reintroduction the first month was considered to be a time of “establishment” in the environment. During the establishment month, home ranges were not randomly located within the landscape, as indicated by the biased occupancy of particular habitat types. Habitat types selected at the landscape scale were similar for familiar and unfamiliar release groups. However, animals released in unfamiliar groups showed a stronger preference for denser high cover habitat during their nocturnal activities within their home range. As tammars use cover to conceal themselves from predators, this result suggests that animals released in unfamiliar groups were more cautious than those released in familiar groups. Indeed at the fine scale, it was also found that animals released in unfamiliar groups were more likely to be found in high cover habitat, and forage closer to cover at night than did those released in pre-established familiar groups. Using habitat with more caution and capitalising on communal vigilance in an unfamiliar habitat may ultimately improve the likelihood of survivorship and overall reintroduction success. Comparing habitat decisions and social behaviours during the establishment period to similar times of year post-establishment suggested that animals' naivety about their new environment influenced some decisions they made. While habitat selection at the landscape scale was similar during establishment and at an equivalent time of year post establishment, analyses showed that they preferred to use melaleuca (a high cover habitat) during their nocturnal activities during establishment much more strongly than they did once they had established. Home range and core areas were also significantly smaller during the establishment month than at an equivalent time of year post establishment. This result supports the idea that animals will restrict their movements when they are unfamiliar with the habitat and predation risks. It also suggests that some habitat choices improved once they were familiar with their new environment and presumably predation risks. Their habitat choices reflected better anti-predator behaviour than those made during the establishment period: they were more likely to use high cover habitat, they remained significantly closer to cover while foraging, and group sizes were larger than during establishment. Seasonal habitat selection at the landscape and home range scales suggested that the five habitat types within the study area provided different fundamental resources for the animals, as they were preferred at different times of year. Some differences in habitat selection were observed between the sexes, and the females were more selective in their diurnal and nocturnal activities. These differences most likely reflected, in part, differences in predator avoidance and reproductive strategies of the sexes, where females' preference at the landscape scale shifted towards high cover habitat during spring, the time of year when pouch young vacate the pouch and start to become independent. While no such selection at the landscape scale was observed for the males, it was also observed that within their daily activities both sexes were more likely to be found in high cover habitat during spring than any other time of the year, perhaps suggesting that as males were following the females. Overall, females generally selected Eucalyptus diversifolia, Acacia anceps and grassland at the landscape scale, and used E.diversifolia for refuge during the day and the other two habitats for foraging at night, whereas males generally preferred Melaleuca halmaturorum instead of E.diversifolia for diurnal refuge. Eucalyptus rugosa was mostly avoided by both sexes. From month to month, both sexes expanded rather than shifted their home ranges to incorporate new areas, and these new areas were explored with conspecifics (when the amount of new area increased the amount of sharing also increased), highlighting their reliance on communal vigilance when in unfamiliar habitat. More new areas were incorporated into home ranges from July to December than from January to May. Time since release was not influential, which also supported the conclusion that perhaps home ranges moved to follow resources or overlap conspecifics more. Indeed, in one circumstance when neighbouring animals had died, a male wallaby was observed to move four kilometres through unfamiliar habitat and completely shift his home range in search of other residence. Compositional analysis of habitat use versus availability indicated that monthly home ranges were selectively positioned in the landscape and were always larger than 4ha. Males' home ranges were larger than females', and males shared more of their home ranges than females did, supporting the usual sex bias observed for polygamous species. Core areas were proportional to the size of the home range, with similar sizes held by males and females and throughout the year. Core size was not influenced by the degree of overlap with conspecifics, with similar amount of core area shared by both sexes year round. The time of year influenced home range size, the smallest were held in winter when food resources were likely to be most abundant, but also when inclement weather was likely to restrict movements, as the animals' ability to detect predators may be hindered due to wet and windy conditions. Living with conspecifics is known to assist predator detection by group vigilance. Indeed, this study found the amount of home range overlap and the time two individuals spend together was positively correlated, and the size of home ranges decreased when more of it was shared with conspecifics, which suggested that sharing of home range was important. The degree which home ranges were shared was observed to be a fairly stable requirement for both sexes and did not change with season or time since release. Despite previous isolation from predators, the wallabies displayed anti-predator behaviours which incorporated interrelated benefits obtained from group vigilance and using protective cover. Additionally, these behaviours were adjusted according to their familiarity with the habitat. Post-establishment, animals were observed to go further from cover when they were a greater distance from their nearest neighbour but surrounded by larger numbers of conspecifics. Whereas during the establishment period, animals ventured further from cover when they were closer to a nearest neighbour, but group size was not influential. It is known that larger groups of animals have more false alarms to predators, and false alarms result in the animals‟ wasting energy in fleeing. If false alarms are more prevalent while occupying unfamiliar habitat with unfamiliar risks, then relying on large numbers of conspecifics while establishing may have been more of a liability than a benefit during the establishment period. However, some anti-predator strategies were commonly used, regardless of familiarity with their habitat. During the establishment month and post-establishment, animals were always more likely to be found in high cover habitat when they were further from their nearest neighbour, or were surrounded by fewer conspecifics. Some strategies and habitat decisions may have reflected differences in reproductive needs. While females, with and without pouch young did not differ in how far they would forage from protective cover, females with pouch young remained closer to their nearest neighbour than those without. This finding perhaps reflected the importance of relying on communal vigilance when their flight time from a predator may be hindered due to increased weight and bulk of a pouch young. These findings supported the theory that group vigilance anti-predator strategies are somewhat innate in the tammars, as having previously been completely isolated from predators their responses could have been lost, and once released there was no opportunity to socially learn the appropriate responses off an established population. Some habitat and social grouping behaviours were occasionally unexpected but may have been balanced out by other behaviours. This study observed that animals foraged further into the open during winter than at any other time of year, which contradicts findings by other authors where tammars foraged further into the open when the weather was fine. However, I also found that animals remained closer to their nearest neighbour during autumn and winter than at any other time of year. Perhaps foraging further into the open in inclement weather is actually safer if it provides a greater chance to detect and react to an approaching predator. For example, a fox approaching from the scrub edge would not give the wallaby enough time to respond. An additional benefit of foraging further away from cover in larger group sizes, is that animals can flee in different directions confusing the fox, as it would have to make a quick decision and chose one animal to pursue. Animals were furthest from their nearest neighbours in spring which was also somewhat surprising as this is when pouch young vacate the pouch and it was observed that females with pouch young remain closer to their nearest neighbour suggesting they gain some anti-predator benefit from doing so. However, during spring the animals were also more likely to be found in high cover habitat than at any other time of year, so this may have somewhat balanced out the need for a close neighbour. Overall, this study confirmed that tammars retain anti-predator behaviours despite previous isolation from predators. However, their habitat and social decisions improved with time since release. In this experimental study, animals released in groups with unfamiliar conspecifics appeared to be at an advantage as they displayed habitat use and social groupings which suggested they were using their new habitat with more caution. Therefore, this study recommends releasing groups of unfamiliar conspecifics. Releasing animals at different times of year also had an influence on how they used their habitat. Animals released in spring displayed behaviours suggesting that they were more cautious in avoiding predators: they were more likely to be found in cover, foraged closer to cover, and were in larger group sizes than those animals released in winter. Therefore, it is recommended that animals are released at a time of year where conditions are fine and resources are abundant. Releasing females with pouch young did not appear to hinder the animals after their release (compared to females without pouch young) and could be recommended as young permanently evacuating the pouch in the wild are at a greater advantage than juveniles released from captivity. Results from this experimental study were used to assist ongoing management decisions and were imperative in the planning of subsequent reintroduction events for this species, and can be applied more generally to other species with similar anti-predator strategies.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2011

The projections from the retina to the visual centres of the brain, such as the dorsal lateral geniculate nucleus and superior colliculus, are organised into retinotopic maps. These maps represent the spatial identity of visual information in the pattern of axonal connections formed and are particularly important for binocular vision, which requires the retinotopically accurate matching of projections from both eyes. Retinotopic guidance cues provide a chemical basis for forming retinotopic maps. Such cues are exemplified by the Eph/ephrin family, though an integrative effect of multiple different cues seems to underlie the formation of retinotopic maps. Ten-m3, a member of the Teneurin family of glycoproteins, is a homophilic transmembrane protein that is prominently expressed in the visual system during development and is a candidate retinotopic guidance cue that has been reported previously to be involved in the formation of binocular maps. The tammar wallaby (Macropus eugenii) is a representative model marsupial macropod, whose protracted ex utero development and sophisticated visual system are highly advantageous traits for the investigation of the developing visual system. These traits allow for the spatially and temporally restricted manipulation of Ten-m3 to investigate its function during development of the visual system in a manner that is not feasible in placental species. This study firstly determined the pattern of expression of mRNA for Ten-m3 in the developing visual system of the wallaby as a basis for subsequently investigating its function. Quantitative polymerase chain reaction found that during development the mRNA for Ten-m3 is higher in ventral than dorsal retina and higher in the retinotopically corresponding medial compared to lateral superior colliculus. It is also expressed at higher levels early in development, compared to later. In situ hybridisation demonstrated retinotopically corresponding gradients of expression of Ten-m3 in these tissues at all developmental ages examined. Specifically, an increasing dorsoventral gradient in retinal ganglion cells was matched to an increasing ventrolateral to dorsomedial gradient in the dorsal lateral geniculate nucleus, and an increasing lateromedial gradient in the superior colliculus. These gradients fit with the expectations of a retinotopic guidance cue and suggest that Ten-m3 could, through homophilic interactions, exert an axon-attractant effect and contribute to the mapping of the dorsoventral retinal axis in these visual centres. Overexpression of Ten-m3 by in vivo electroporation in nasal subregions of the retina and tracing projections from the whole eye showed no detectable effects on contralateral retinal projections. Rather, ipsilateral projections to the future binocular (medial and rostral) colliculus were increased, fitting with the proposal that Ten-m3 mediates mapping by axon-attractant homophilic interactions. Depending on the nasal subregion of the retina targeted, the ipsilateral retinogeniculate projection extended ventrolaterally, beyond the normal dorsal binocular zone of the nucleus. The changes mediated by increased levels of Ten-m3 could be due to either recruiting more ganglion cells to project ipsilaterally, or by specifically changing the behaviour of existing ipsilaterally projecting ganglion cells. The findings described in this thesis complement studies in the Ten-m3 knockout mouse and suggest that the role of Ten-m3 in contributing to the binocular retinal map is conserved between marsupial and placental mammalian species.

The skin extracts from amphibians have been investigated for over fifty years and have been found to contain numerous components with therapeutic and medicinal uses. Host - defence compounds are secreted onto the dorsal surface of the animal from specialised granular glands in response to a variety of stimuli, such as stress induced by a predator. Isolated peptides can exhibit either pharmacological properties or antibiotic activity. Previous studies isolated a potent hypotensive neuropeptide, crinia angiotensin II, within skin secretions of the Australian frog Crinia georgiana. This prompted further investigations into the isolation and sequence determination of host - defence compounds from other species in this genus - C. signifera, C. riparia and C. deserticola. Fifteen novel peptides were identified. The major peptide components were potent disulfide containing neuropeptides of a type not observed in other Australian anurans that have been previously investigated. The remaining peptides demonstrate either antibiotic activity or inhibit the enzyme neuronal nitric oxide synthase. The skin components from anurans of the Litoria genus have been extensively studied, with a number of peptides exhibiting both antibacterial and pharmacological activity. The skin secretion of Litoria dentata has been investigated, with five novel peptides identified. The neuropeptide tryptophyllin L 1.3 was previously isolated from the related frog L. rubella. Other components that are unique in structure have not yet been tested for biological activity. The parasitic disease malaria is responsible for over one million deaths per year. The increase in resistance of current antimalarial compounds has led to the development of new treatments from various animal - derived peptide antimicrobials. A number of amphibian peptides and their derivatives were investigated as potential antiplasmodial agents against the malaria parasite Plasmodium falciparum. Results indicate that these compounds inhibit parasite growth with minimal haemolytic activity, making them promising tools for malaria research.The defence chemistry of amphibian neuropeptides has been extensively studied and is important in understanding both the ecology and physiology of the vertebrate. Neuropeptides are classified into groups with similar structural characteristics. Biological activity occurs via interaction with a G protein - coupled receptor. The most studied of all amphibian neuropeptides is caerulein, which has a similar spectrum of activity to the mammalian peptide cholecystokinin. This includes smooth muscle contraction that occurs via interaction with cholecystokinin receptors. The pharmacological activity of Australian anuran neuropeptides from various genera was investigated. Two biological assays were conducted - a smooth muscle contraction test and a lymphocyte proliferation assay. A range of neuropeptides contracted smooth muscle at nanomolar concentrations, while others only proliferated lymphocytes. Some peptides were inactive in both assays. Young marsupials are born at an immature stage of development and rely on immune protection provided by the mother. Eugenin is a host - defence compound isolated from pouch secretions of the Tammar wallaby. The immunomodulator activates CCK2 receptors, resulting in lymphocyte proliferation. Therefore, eugenin stimulates immune cells in the pouch providing vital immune protection for pouch young.
Thesis (Ph.D.)--School of Chemistry and Physics, 2006.

Comparisons between the genomes have provided invaluable resources and tools for the annotation of DNA sequences. Comparative genomics is widely used to identify function of DNA sequences, understand dynamics of the evolutionary processes and provide framework for genome organization. Particularly useful for comparative analyses are the genomes of distantly related organisms such as marsupials and human. When the DNA sequence data was scarce and expensive to acquire, comparative analyses of genomes were performed by comparative gene mapping studies. However, with the advent of cheaper and faster DNA sequencing technology, genome scale comparisons at a single nucleotide level were made possible. This cheaper and faster DNA sequencing has resulted in an avalanche of information available for comparative analysis. A major challenge of comparative analysis is to explore genome organization and evolution by locating the markers on the chromosome. This has traditionally been achieved by genetic linkage and physical maps, which are generated by different experiments and not always easy to align. I have pioneered a strategy to characterize the low coverage genome sequences, which were subsequently used for identifying microsatellite markers for the tammar wallaby linkage map. My strategy allowed for easy integration of the physical map and linkage map to construct an integrated map of the tammar wallaby genome. Specifically, I first identified and used conserved blocks of synteny between opossum and human, which were reconstructed for tammar wallaby by overlapping sequence searches and assembly process. These reconstructed conserved blocks of synteny were then assigned to tammar wallaby chromosomes using the physical mapping data. Since tammar wallaby linkage groups have previously been assigned to chromosomes, the gap regions and corresponding conserved blocks of synteny were easily identified from the karyotype. Subsequently microsatellite markers were sought in the conserved blocks of synteny and tested for polymorphism in the mapping families. 26 targeted markers were finally used for linkage analysis. This systematic use and characterization of the low coverage genome sequences led to a great saving in cost and effort for obtaining high quality linkage map (150 markers), which will be used for the assembly of the low coverage sequences. Once the assemblies of the genomes are produced, they can be used to infer fine scale karyotype rearrangements that occurred during the evolution of chromosomes. For instance, comparisons of the sex chromosomes between the three major groups of mammals (placental, marsupial and monotreme) has led to a new understanding of how human sex chromosomes evolved from two genome blocks, one representing a conserved therian X (XCR) and one a region added in the placental lineage (XAR). A recent study involving genome assembly comparisons, in which the human Xchromosome genes were compared with the chicken genome, concluded that the human X chromosome is composed of three evolutionary layers. This conclusion was inconsistent with the widely accepted model proposing only two evolutionary layers, the X-conserved region and the X-added region. I therefore investigated the origins of the genome blocks making up the human X chromosome to identify the cause of this inconsistency and resolve it. My comparative analysis of the location and order of the human X chromosome homologous genes in rat, opossum and chicken genomes revealed that the problem arose because of inaccurate assignment of chicken paralogs as the orthologs. I identified the true orthologs of the human X genes in the chicken/zebrafinch EST database and showed that paralogs were incorrectly identified because the orthologs were missing from an incomplete chicken genome assembly. I then mapped the orthologs of human X genes in tammar wallaby by using the fluorescent in situ hybridization, and compared them with platypus, chicken, lizard and frog genomes to conclude that the human X chromosome is composed of only two evolutionary layers, the X-added region and the X-conserved region, as originally proposed. The assignment of orthologous or paralogous relationships in order to track gene evolution is particularly difficult for genes that belong to large families. In the last part of my research I analysed a huge and rather unusual gene family, the olfactory receptor gene (ORG) family. Comparative analysis of ORGs is difficult because the family is extremely large (~1000 genes in mammals). No comprehensive analyses have yet been performed to identify and characterize members of this gene family in a systematic fashion since the advent of large-scale genome sequence data. Therefore, I performed exhaustive searches to first identify olfactory receptor genes in all vertebrates. There are approximately 1000 olfactory receptor genes in mammals and frog, 500 in birds and 150 in lizards and fish. I also classified this gene family in 101 evolutionarily related groups of genes to provide a framework for dissecting evolutionary pathways. I also proposed a systematic nomenclature for this gene family based on the classification. This specialist data mining and classification strategy for olfactory receptor genes will provide unique opportunities to advance our understanding of this gene family in the future.

The XX female/XY male sex chromosome system of therian mammals evolved from a homologous pair of autosomes following evolution of a testis-determining factor on the Y chromosome. Over time, male-advantage alleles accumulated around the sex-determining locus leading to suppression of recombination between the X and Y to preserve the male specificity of this region. In the absence of recombination, the Y chromosome serially degraded, resulting in the dimorphic sex chromosomes seen in extant mammals. The highly heterochromatic Y makes traditional "shotgun sequencing" impractical and therefore very few Y chromosomes have been studied in detail. Most knowledge of Y chromosome gene content and structure comes from eutherian mammals. Marsupials occupy a particularly informative phylogenetic position between the bird-mammal divergence and eutherian radiation with the marsupial Y evolving independently from the eutherian Y for 148 million years. In order to understand how the therian Y chromosome has evolved, I focussed on the Y chromosome of an Australian marsupial, the tammar wallaby (Macropus eugenii). The isolation of Y chromosome specific sequences is key to expanding our knowledge of the marsupial Y chromosome. I isolated and characterised clones from a testis cDNA library and two male tammar wallaby BAC libraries using a microdissection derived Y chromosome probe as well as three-dimensional PCR screening. Because the long arm of the tammar wallaby Y chromosome is known to contain heterochromatic sequences shared with the short-arm of the X chromosome, efforts were focussed on the short-arm of the Y to examine the location and arrangement of genes. I identified four novel genes on the tammar wallaby Y, expanding my work to other marsupials to demonstrate that there are at least ten genes which are X/Y shared in three orders of marsupials. This enabled me to develop a model to describe the evolution of the marsupial Y chromosome. The tammar wallaby Y chromosome appears to be an intricate mixture of different repetitive elements; highly iterated elements found throughout the genome, X-Y specific repeats derived from the remnants of a shared NOR and Y-specific repetitive elements. This study catalogued 39 BAC clones mapping to the tammar wallaby Y revealing the structure of the Y to be a convoluted mixture of simple repeats, more complex repetitive elements shared with the X as well as Y-chromosome specific elements, all providing the framework within which the small number of Y genes reside. The gene repertoire of the marsupial Y chromosome implies that multifunctional genes on the proto XY were retained and subsequently specialised on the therian Y, as evidenced by the involvement of human and mouse X-borne homologues (of marsupial Y genes) in brain and testis function. The marsupial Y chromosome has degraded in parallel with the eutherian Y. The common therian ancestor had a Y chromosome with at least twelve X-Y shared genes. Some of these genes evolved male-specific functions and are found today on the Y chromosomes of various marsupial and eutherian mammals. Other genes were gradually pseudogenised and ultimately lost from the Y chromosome in a lineage specific fashion.

GnRH-targeted immunocontraception has potential as a non-lethal means of managing overabundant native species in Australia, and also represents a useful tool for studying the key processes within the reproductive endocrine axis. In this thesis, the effects of the GnRH vaccine 'GonaCon(TM)' on peri-pubertal development, growth, adult fertility and social behaviour are examined in two model macropodid species, the tammar wallaby, Macropus eugenii and the eastern grey kangaroo, M. giganteus. Vaccination against GnRH in adult male tammars resulted in rapid testicular atrophy and a loss of fertility for a minimum of two years in association with the production of significant GnRH antibody titres. Puberty was also delayed for a minimum of two years following vaccination of immature males of this species. Male-type growth rates were suppressed in association with depressed testosterone production in males of both age groups, and significant interruptions to both sexual and agonistic behaviours were observed in both adult- and juvenile-treated males. In females, GnRH vaccination effectively suppressed reproduction in 100% of adult female tammars over 5 breeding seasons. Treatment had no apparent effect on lactation but inhibited the production of young from diapausing blastocysts in this group, possibly by via some effect on the corpus luteum of pregnancy. Vaccinated sub-adult female eastern grey kangaroos failed to undergo normal peripubertal development (based on observations of pouch condition) and remained reproductively inactive for the duration of the study (2 1/2 years) - unlike Controls which all produced pouch young. No significant impacts on animal health or welfare were observed during this study however the effects of altered behavioural interactions will need to be re-evaluated on a larger scale to ascertain the potential for any negative impacts on animal welfare or the attainment of management objectives. Based on the long-lasting and highly efficacious results observed, GnRH-targeted immunocontraception would likely be a useful means of managing urban macropodid populations.