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Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, Science, Environment, Engineering and Technology, The earth is undergoing its sixth mass extinction event. This biodiversity crisis is directly attributable to anthropogenic disruptions of ecosystem processes. These disruptions include extracting and killing organisms, clearing habitat, introducing exotic species and disrupting climate at a global-scale. Connectivity is an attribute of both populations and ecosystems which, when disrupted, leads to fragmentation. Fragmented systems often have lower ecological functioning and resilience than connected systems. The maintenance of natural rates of ecological connectivity is a major challenge. Mangroves are intertidal forests which grow along the subtropical and tropical coasts of the world. These forests are extremely valuable; maintaining coastal water quality, protecting shorelines from severe weather events, providing habitat for fisheries species and iconic megafauna, and sequestering blue carbon. Unfortunately, mangrove forests also remain vulnerable to the many human activities competing for space in the coastal zone, and to the effects of sea-level rise (SLR). One of the keys to ensuring mangrove conservation and functioning into the future is a thorough understanding of the connectivity and fragmentation of these systems. This thesis consists of four studies. The first is a comprehensive review of research on marine population connectivity. This study identified that intertidal wetlands are particularly under-represented in the marine connectivity literature. This chapter led to the remaining three chapters which assess fragmentation and connectivity in mangroves. The first of these is a mark-recapture experiment which considers connectivity at the population level. I modelled intra-forest dispersal of mangrove propagules as the interaction between propagule and habitat attributes. I identified interactions and thresholds that determine the capacity for propagules to disperse efficiently. The other two chapters consider mangrove fragmentation at a landscape le

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, Science, Environment, Engineering and Technology, Freshwater ecosystems represent hotspots for the world’s total diversity and human well-being. However, they are also subjected to threats across the globe as a result of localised human activities, broad scale catchment clearance, climate change and invasive species. The increased degradation of freshwater habitats and their ecological functions as a consequence of these threats, at local and global scales, has led to significant freshwater problems for human existence and the world’s biodiversity. There is growing evidence that the loss of biodiversity is one of the most complex environmental issues facing the world; however, the importance of understanding species distribution patterns and the ecological differentiation among species that are reflected as species-specific responses or tolerances to environmental drivers is less well understood. In particular, when a morphological approach is used as a taxonomic tool for investigating species diversity and species level responses to environmental drivers, the diversity of responses hidden within species complexes may not be realized, and the conclusion of generality may mask specific cryptic species responses. In South-East Queensland, Australia, European occupation since the mid 1800’s has seen large scale clearing of native vegetation along streams and rivers in nearly all catchments. As a consequence of this land-use change catchment hydrology has been substantially altered, which, combined with the presence of dams and weirs, has resulted in a decline in water quality of streams in some catchments, which is of growing concern for conservation of species biodiversity. This study aimed to explore cryptic diversity in two species complexes of freshwater aytid shrimps common in South-East Queensland and elucidate species level responses to environmental variation that could explain their spatial distribution. This broad aim was met through three specific studies. First, using regional scale data of cryptic species

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, Science, Environment, Engineering and Technology, Microplastics (i.e., plastics particles < 5mm) are widespread emerging contaminants that have been detected in various aquatic environments worldwide including freshwater and marine ecosystems. Contamination of the environment with microplastics has become an environmental issue due to the potential of plastics to remain for thousands of years and to accumulate in the aquatic environment. The abundance of microplastics in the aquatic environment is assumed to increase due to continuous fragmentation of macro and microplastic debris, which can lead to a decrease in the average size ranges of microplastics over time (Cole et al., 2011). Moreover, concerns have been raised regarding the potential of microplastics to physically (e.g., blockage of digestive tract) and chemically (e.g., leaching of sorbed chemicals and toxic additives) harm aquatic organisms. Microplastics can enter the aquatic environment from both aquatic-based and landbased sources. Recently, wastewater treatment plants (WWTP) have been identified as one of the important land-based sources of microplastics. While microplastics have been reported in WWTP effluent in Asia, Europe, USA and Russia, little is known about the presence of microplastics in Australian WWTP effluent. More importantly, the lack of standardized techniques to sample and characterize microplastics in environmental samples, especially in complex samples such as wastewater, has led to inaccurate estimations of microplastic concentrations. In response to the current knowledge gaps, a novel validated high-volume sampling device was developed for in situ fractionation of microplastics from wastewater effluent as part of this project. The developed method was applied to three Australian WWTPs utilizing primary, secondary and tertiary treatments to provide a snapshot of the fate and removal of microplastics during various wastewater treatment processes. To achieve an accurate estimation of microplastics, the sampling technique was combined

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, Science, Environment, Engineering and Technology, Generally freshwater fish exhibit higher levels of genetic structuring between spatially distinct populations than marine species due to the presence of natural and artificial barriers to dispersal in freshwater ecosystems. In addition, freshwater species are not able to move between populations that are separated by either terrestrial or marine habitat. Diadromy constrains the development of genetic structuring, even among geographically isolated populations due to potential connectivity via movement through the sea. As a result, higher levels of gene flow and lower population structuring tend to be observed in diadromous fishes than freshwater species. The Australian smelt (Retropinna semoni) is a native fish species complex widely distributed across coastal and inland drainages of south-eastern Australia. Recently, a complex of five or more cryptic species of Australian smelt has been recognized throughout their geographic range based on genetic studies. Variation in life history strategies has been observed in many cryptic fish species and multiple life history patterns were also found in southern smelt lineages (Retropinna sp.) where mainland Australian populations contain diadromous and wholly freshwater individuals and Tasmanian populations contain estuarine individuals. Despite the populations of southern smelt containing diadromous individuals, strong genetic structuring and low levels of connectivity were reported in at least some populations, which were suggested to result from apparently diadromous individuals being retained in the estuaries. It is possible that the different cryptic species may differ in life history. In the present study, I examine the genetic structure and life history variation of the South-east Queensland (SEQ) lineage of Australian smelt which was further subdivided into northern and southern lineages (SEQ-N, SEQ-S). I used both molecular and ecological approaches to understand the pattern of genetic structure and life history vari

Full Text, Thesis (Masters), Master of Philosophy (MPhil), School of Environment and Sc, Science, Environment, Engineering and Technology, Species of Charopidae from mid-eastern Queensland in the collections of the Queensland and Australian Museums were reviewed primarily using aspects of shell morphology. Protoconch sculpture played a key role in this revision and 261 protoconchs were examined by scanning electron microscopy in order to develop a basic terminology that could be used in descriptions of genera and species. Eleven baseline patterns, some with subtle variations, were established. Eight of these are shown to be present in mid-eastern Queensland Charopidae. Studies of protoconch and teleoconch sculpture combined with shell coiling patterns showed that a number of genera and species, many newly documented, are represented. A cladistic analysis using a range of shell measurements was conducted to confirm these results. Additional verification, though limited, was sought through molecular analysis where animal tissue was available. Anatomical dissection of the male genitalia was performed on specimens of two species for which adequate preserved material was available. From an initial 13 known species, thirty-nine species of charopid are documented including a reallocation of the three ‘Gyrocochlea’ species currently described from the region resulting in three new genera, Whitcochlea gen. nov., Stanisicaropa gen. nov. and Radiolaropa gen. nov., and a new species, Radiolaropa eungella sp. nov. An additional four new Gyrocochlea-grade species are described in four new genera, Amfractaropa gen. nov., Comularopa gen. nov. Nodularopa gen. nov., and Xenoropa gen. nov. The genera Isolderopa Stanisic 2010 and Pereduropa Stanisic 2010 are expanded with the description of six new species. A new genus, Tristanoropa gen. nov. is diagnosed for the inclusion of three new species. Twelve additional species, some based on damaged specimens, are briefly described in order to complete the inventory. The majority of mid-eastern Queensland species appear to be endemic to the region. Biogeographical discussions fo

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, School of Environment and Sc, Science, Environment, Engineering and Technology, The spider infraorder Mygalomorphae includes the funnel-web spiders, tarantulas, trapdoor spiders and their kin. Because of their particular life history characteristics, systematic revisions of mygalomorph taxa are fundamentally informative and of broader biological interest, but also a matter of conservation priority. Mygalomorph spiders are relatively long-lived, usually with limited dispersal abilities, high habitat specificity, and a long historical presence in areas relative to landscape processes. These characteristics lead to high levels of speciation and local endemism in many mygalomorph lineages, and a build-up of genetic structure between and within species at fine spatial scales. From the perspective of a researcher, high levels of genetic structure and speciation make mygalomorph lineages ideal for investigating biogeographic history and speciation processes. From a conservation perspective, local endemism, habitat specificity and low dispersal ability mean that mygalomorph populations (and potentially species) are sensitive to habitat modification, and have little ability to disperse from, or recolonise, affected areas. In the context of a biodiversity crisis, and hindered by ‘impediments’ to systematics and taxonomy, systematists must allocate their time and efforts carefully. Given their inherent vulnerability and the value of research on mygalomorph taxa, revisions of poorly known elements of this fauna are both urgent and of evolutionary importance. Intergeneric relationships within the spiny trapdoor spiders of Australasia (Idiopidae: Arbanitinae) were recently stabilised. This provided a foundation for targeted work into genera within the subfamily, many of which had never received substantial systematic attention. Prior to my project, only seven species of golden trapdoor spider (tribe Euoplini, previously all in the genus Euoplos) had been described from eastern Australia, despite the genus spanning the length and breadth of the eastern mesic

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Bengal tiger (Panthera tigris) is an endangered species found in the lowland areas of Nepal. Much needs to be understood about this species, including its population size, genetic health, habitat and overall ecosystem dynamics. Although there have been efforts to estimate tiger population numbers using camera trapping methods, the information obtained through such efforts has been limited and there is a need to find a better method and technology to understand wild tigers in Nepal. Use of genetic sampling holds significant promise in execution of landscape-level management plans as it may allow managers to measure genetic health and even gene flow with greater certainty. Habitat connectivity and the degree of movement from one habitat patch to another can be inferred through understanding of species behavior, but genetic data can give us landscape level information by directly identifying patterns of distinctiveness, endemism and the degree to which gene flow exists between subpopulations. Non-invasive genetic studies on populations, such as those that use scat samples, have increased in recent years, and have been used to estimate population size of many elusive and endangered species. I have used this technique to understand tiger and its habitat. In my study I have uncovered prevalent sympatric biodiversity in the tiger habitat which aids in understanding the species conservation from an ecological perspective. Out of total collected scat samples (n=420), only 56% (n=237) were of tiger. The remaining non-tiger samples (n=183) included non-focal carnivores; leopard (Panthera pardus, n=83), leopard cat (Prionailurus bengalensis, n=10), jungle cat (Felis chaus, n=2), fishing cat (Prionailurus viverrinus, n=2) and fox (Vulpes spp., n=10). The spatial distribution of three small felids: leopard cat, jungle cat and fishing cat in sub-tropical deciduous forest of Terai has provided insights on sympatric occurrences of small cats with each other and with two other large

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Population genetics provides a framework for understanding genetic drift, mutation, migration and selection in natural populations. In the past, population geneticists concentrated on a handful of markers due to limitations of technology. However, with the advancement of Next Generation Sequencing Techniques, the field of population genomics has emerged, which facilitates understanding of evolutionary processes at a genomic level. Any population genetic measure which used to be just a point estimate can now be estimated across the genome. In addition to calculating genome wide averages for genetic differentiation among populations, we can also identify specific regions of the genome under natural selection. It has been of great interest to study natural selection in populations adapted to different environmental conditions and with the development of the technology this has become more feasible. Due to global climate change, species need to adapt to the changing environment and this is only possible if there is sufficient adaptive genetic variation at the molecular level. Adaptive divergence among populations has been studied across different altitudes, in different host forms, along latitudinal clines and between different coastal thermal regimes. This thesis is focused on the species Paratya australiensis which consists of 9 highly divergent mtDNA lineages. Lineage 4 and Lineage 6 of this species have been observed to have preference for upstream and downstream respectively and have been suggested to be adapted to different temperature regimes. In order to evaluate this, I have used a genomic approach in this thesis to investigate population structuring and evidence of adaptation between upstream and downstream populations of P. australiensis in the Mary River catchment in south east Queensland, Australia. My thesis has focused on a single lineage, lineage 4. Three streams (Broken Bridge, Booloumba and Obi Obi Creek) within the Mary River catchment were selected f

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, It is now widely understood that species boundaries are often semipermeable, and that hybridisation and introgression occur frequently in nature and have the potential to dramatically alter the evolutionary trajectory of the taxa involved. Hybrid zones, regions where genetically distinct populations overlap and produce hybrid offspring, provide a valuable opportunity to gain insight into the speciation process. They can arise without a period of isolation when distributions span environmental gradients or ecotones (primary hybrid zone), or as a result of secondary contact following allopatric divergence (secondary hybrid zone), and their structure and ultimate evolutionary outcome can vary greatly depending on the strength of pre- and post-mating barriers to gene flow, as well as the impact of other evolutionary forces (e.g. selection). The dawn of the age of genomics offers great possibility for the analysis of potentially hybridising taxa. In this thesis, I employ a genomic approach alongside more traditional molecular and non-molecular techniques to examine the presence and influence of hybridisation on two native Australian parrot species, the pale-headed (Platycercus adscitus) and eastern rosellas (P. eximius). Together, these species, which are each composed of readily identifiable subspecies, span the eastern seaboard of Australia, with species and subspecies reportedly hybridising where their ranges overlap.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Many species exhibit some form of colour variation between groups or individuals, and studies of such colour variation, its genetic basis and functional importance can contribute unique insights into the evolutionary, ecological, demographic and genetic processes affecting the diversity of life. Through the examination of the genetics underlying colour traits, the relative importance of different selective and demographic processes in the evolution and maintenance of a trait can be inferred, enabling scientists to gain a better understanding of what drives evolutionary change in different organisms and environments. Such studies also assist in bridging the gaps in our knowledge about the interactions between genetics and ecology that are involved in phenotypic variation. Understanding the pathways linking genetic and regulatory changes to phenotypic change and evolutionary change through time contributes to our knowledge about how species develop and evolve. The Australian magpie (Cracticus tibicen), is a group-living and territorial passerine bird with a characteristic pied appearance of strongly contrasting patches of black and white plumage. The species has several different plumage forms, delineated by the colour and/or pattern of back feathers; these plumage forms hybridise where their distributions overlap. Distributions of plumage forms are highly discordant with patterns of phylogeographic structure found in this species, making a scenario of allopatric divergence followed by secondary recontact at hybrid zones highly unlikely.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Gradients in altitude are used frequently to understand how species respond to changes in local climatic conditions and are therefore a robust tool for predicting how species and communities in montane environments may respond to changes in climate. It is important that we understand how species richness patterns and interactions are affected by current changes in climate if we are to make sensible predictions about how biodiversity and ecosystem function will be affected by climate change. Further, while studies have shown a strong gradients in species richness and species turnover that accompany altitude, little is known about how species at different heights in forests and how plant-insect herbivore interactions respond to altitude. This challenge has been addressed here by examining the changing distribution patterns of the taxonomic group, Auchenorrhyncha, which are an important group of plant sucking herbivores, with altitude, in vertical forest columns and of their associated host plants. Herbivorous insects, including leafhoppers and planthoppers interact with their host plants in complex networks, but relatively little is known about how these relationships will be and are being affected by changes in climate. In order to determine how altitudinal changes in climatic conditions affect distribution patterns of Auchenorrhyncha, I quantified these communities along two altitudinal gradients, one in eastern Australian subtropical rainforest and the other in northern Australian tropical rainforest.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Freshwater fishes are often characterized by extensive population genetic subdivision and low genetic diversity and are ideal subjects for investigating contemporary patterns of dispersal and subsequent gene flow. In lotic systems, different riverine architecture, variable hydrology and species biology influence genetic diversity and population structure in resident species. Stream-dwelling species often display greater levels of gene flow within drainages or catchments or sub-catchments than between them due to complexity of stream order and the isolating nature of these systems by land or sea. However, the relative importance of these attributes in driving population structure at spatial scales remains poorly understood for many freshwater species. Study on the effects of riverscape in shaping population structure is very important to identify management or conservation units and to undertake habitat restoration measures. The Daly River is one of the largest river networks in the wet-dry tropics of Northern Australia and shows variability in hydrology. This river has a complex arrangement of habitats and heterogeneous landscape features (e.g. slope, elevation) across the catchment area. There are also instream physical barriers like waterfalls, cliffs, road crossings etc. that may hinder dispersal and subsequent gene flow.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, The overall aim of this project was to consider several freshwater invertebrates that are restricted both geographically and climatically to determine their population genetic structure, population distribution and population viability. The study was set in a framework of genetic analysis as genetics can be used to answer a whole suite of conservation focused questions. Specifically, the study concentrated on the population dynamics of three freshwater crayfish from the genus Euastacus: E. hystricosus, E. urospinosus and E. robertsi. Also, in this study I explored the role of two commensal flatworms as proxy species, to aid in disentangling the population structure of their crayfish hosts. These flatworms were Temnosewellia batiola, which is specific to E. hystricosus and Temnosewellia albata, which is specific to E. robertsi. As part of this study, the known distribution of E. urospinosus was increased from 200 km2 to 1225 km2 in area with 26 locations being identified in the Brisbane and Mary River catchments of SE Queensland, Australia (Hurry et al. 2015 Chapter three). Calculations that were undertaken after publication with the ALA (2015) online tool have now calculated an area of occupancy of approximately 76 km2 or an extent of occurrence of 610 km2. Further, mitochondrial DNA sequence data were then used to investigate the population structure and the phylogeographic divergence between four uplands. There was significant population differentiation for the species which conforms to the headwater model of genetic structure. Fragmentation between these uplands was found to be historical as the first divergence between lineages was dated at ~2.1 million years ago (mya).

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, The overall aim of this thesis was to investigate the morphological and molecular diversity within Tenuibranchiurus, and to utilise these data to further the understanding of the evolution of this freshwater crayfish and the other genera of the Australian burrowing clade from both a phylogenetic and biogeographic perspective. The genus Tenuibranchiurus occurs within coastal eastern Australia and currently represents the largest gap in knowledge within this clade of crayfish. It is also the only monotypic parastacid genus, containing the single species T. glypticus. Additionally, it has morphological, phylogenetic, and geographical attributes that are not exhibited by other members of the burrowing clade, or by other freshwater fauna found throughout its distributional range. Examination and clarification of these unique features has the potential to elucidate evolutionary processes determining the distribution and genetic structure of the genus, the burrowing clade, and the freshwater fauna of coastal eastern Australia.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Throughout history, climatic changes have caused environmental systems to shift and have influenced biotic assemblages. Most of these changes have occurred slowly, over millions of years, enabling species to either adapt to new conditions, endure the changes, or shift distributions to maintain their habitat requirements. Due to the fast rate at which climate change is currently occurring, it is unknown if species will be able to use these mechanisms to successfully respond to this rapidly changing environment. Areas that have small geographical extents, elevated uplands and high numbers of endemic species, such as the Wet Tropics in north-eastern Queensland, are expected to be particularly vulnerable to climate change. The endemic species in this at-risk area are also expected to be more susceptible to climate change. The endemic Boyd’s forest dragon (Hypsilurus boydii, Macleay) is a highly camouflaged, large lizard that inhabits lowland and upland forests from the northern to the southern boundary of the Wet Tropics. Determining how H. boydii has responded to previous climate change may give insight into how the species may respond to future climatic changes. The main aims of this study were to understand how geographical features and climate have influenced the genetic makeup, morphology and distribution of H. boydii, and to use this information to determine how climate change may influence future populations. This study used genetic analyses to identify evolutionary and geographical relationships across the Wet Tropics (north vs. south of the Black Mountain corridor [BMC] and upland vs. lowland) and within each of these regions; explore morphological variation across the regions and examine conformity to three eco-geographical rules (Bergmann’s rule, Allen’s rule, and the isolation rule); and attempt to predict species distribution patterns of the species throughout the Wet Tropics during past, present and future climatic scenarios. Seventy-seven dragons were col

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Anthropogenic disturbance regimes in areas that were once large continuous habitats have been major drivers of habitat fragmentation and loss which in turn form the largest worldwide threat to biodiversity. Studies suggest that functional trait based approaches provide better understanding of fragmentation effects on ecological processes in human- modified landscapes. However, research on these thematic areas is limited in many tropical regions, such as Ethiopia. In the second chapter of this thesis, I evaluated sensitivity of bird communities and functional groups to fragmentation processes in Ethiopia. Standard point counts were used to survey birds in 16 remnant forest patches of variable sizes and degrees of isolation. The information theoretic model selection approach was used for precise understanding of avian functional group responses to habitat loss and fragmentation. Results showed strong impacts of forest loss and fragmentation on forest specialists, insectivores, frugivores, open nesters, understorey nesters and resident birds. These results led to the identification of indicator bird functional groups, which can be used to prioritize sites for conservation particularly where management funds are limited. Specifically, the indicator groups can provide the cheapest option to efficiently conserve biodiversity of the region particularly when systematic conservation planning approaches are used while at the same time considering important landscape features, socio-economic, political and bioclimatic factors. Where management resources are affordable, protection and restoration of the remnant forest patches and matrix vegetation may help mitigate the negative effects of fragmentation on the specialist bird functional groups.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Freshwater crayfish are a highly diverse group of decapod crustaceans that are distributed across all but the Indian and Antarctic continents. Their broad distribution suggests a strong ability to disperse and adapt to a wide range of habitats and environmental niches. In particular, freshwater crayfish have been discovered in caves, burrows, streams, lakes and sometimes even terrestrial habitats. This dispersed distribution across a range of habitats is particularly evident for the genus Cherax, with at least 47 species identified from throughout Australia. With some species highly diverse and others widely distributed, it is unclear what effect geographic, behavioural and ecological isolation has had on the current biogeographic structure of Australian Cherax. By investigating variation across a nested series of scales, the primary aim of this study was to distinguish the historical and contemporary drivers that may have caused and maintained the high level of biodiversity observed in Australian and more specifically South-East Queensland (SEQ) Cherax.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Nearly one fifth of Australia’s continent is covered by forests, including 147.4 million hectares of native forest and 2.0 million hectares of forestry plantations. Australia has about 4 percent of the world’s forests on 5 percent of the world’s land area. Prescribed burning has been extensively applied to manage forest fuels in Australia since the 1960s. It greatly decreases the wildfire hazard, promotes forest regeneration and controls insects and disease. Fire modifies both the above-ground vegetation and below-ground microbial community. Despite the significant role of prescribed burning in nitrogen (N) dynamics, most studies have focused only on the responses of one or several forest components (e.g. vegetation, microbial community or soil nutrients) to fire separately. Few studies have offered an in-depth insight into the relationship between soil N cycling processes and associated functional communities in response to long-term prescribed burning. Denitrification is an important part of forest N cycling. It is a stepwise dissimilative reduction process of nitrate (NO3-) to dinitrogen gas (N2) under anaerobic conditions and the primary pathway of nitrous oxide (N2O) emission from soil. This gaseous product has a global warming potential about 298 times greater than that of carbon dioxide (CO2). The potential environmental implication of denitrification to global warming has drawn increasing scientific attention worldwide. A variety of microbial functional groups participate in the denitrification process and each of them can be measured by targeting one or more specific functional genes.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Comparative phylogeography seeks to compare phylogeographic patterns of multiple co-distributed species in order to examine levels of temporal and spatial congruence. Comparative assessments can lead to reconstructions of major trends in the recent histories of dispersal of a region and can provide significant advances in understanding how behaviour, demography and natural histories of species and populations can influence phylogeographic patterns. When common spatial patterns of evolutionary sub-division are found between co-distributed species they are thought to share a biogeographic history. Although concordant phylogeographic patterns have been found across multiple taxa, not all comparative phylogeographic studies have found evidence of congruence. The influence of dispersal potential on the phylogeographic structuring of multiple co-distributed species was the main focus of this thesis. The main goal was to explore how dispersal potential, based on life history characteristics, influenced phylogeographic structure on a large-scale in multiple co-distributed species, and in particular how this influenced oceanic island populations. Whilst there are disagreements in the biogeographic literature as to whether vicariant or dispersal processes best explain the geographic distribution of a species, the colonisation and accumulation of biotic assemblages on oceanic islands is unequivocally the result of transoceanic dispersal. The biotic communities present on oceanic islands therefore inevitably consist of species that are able to disperse well. Genetic variation within island populations is directly influenced by the dispersal potential of the species in question. Species that disperse frequently will be more closely related to the source population due to continual migration to the islands from mainland (or other island) sources; whereas species that do not disperse as often will be more genetically distinct and divergent from the source population.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Mutations give rise to the variation that is seen across all levels of biological organisation. Microevolution, i.e. the collective process that changes allele frequencies in populations, acts on the lower levels of the hierarchy of levels of biological organisation and operates over short timescales. Thus microevolutionary studies represent the basis for evolution at the population and species level. This thesis investigates how microevolution acts on different levels of biological organisation, i.e. molecule (Section 6), organelle (Section 5), cell (Section 5), tissue (Section 5), organism (Section 5), population (Section 3 & 4) and species (Section 2). Mitochondrial DNA is commonly used in population and conservation genetics studies because of its high mutation rate that typically translates into high resolution analyses of evolutionary mechanisms and processes over short time scales. Two different methods are presented that facilitate the recovery of complete mitochondrial genomes. The first uses only three primer pairs and is designed to amplify the mitochondrial genome for any avian species. The method can be adapted to amplify the mitochondrial genomes for any animal class using the super conserved prime site principle. The second method uses the endonuclease RecBCD to digest the linearised nuclear DNA in a whole blood DNA extract, leaving only the circular mitochondrial genomes. This method is potentially applicable to the study of any animal species and has the advantage of recovering the true mitochondrial genotype frequencies, due to the absence of amplification bias. Both methods can thus greatly facilitate the recovery and characterisation of mitochondrial genomes in combination with second generation sequencing. The recovery of complete mitochondrial genomes allows the study of microevolution at high resolution and thus increases confidence in subsequent analyses.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, The chestnut-shouldered fairy-wrens comprise a subgroup of four species in the genus Malurus (Passeriformes: Maluridae). Collectively, they are widespread across the Australian continent but phenotypic variation is strongly structured geographically in just one species, M. lamberti. Earlier phylogenetic analyses of this group have been limited to one or two individuals for each species and have not represented all currently recognized subspecies of M. lamberti. Historically, the taxonomy and nomenclature of the M. lamberti complex has been debated, in part because of morphological similarities among its subspecies and another member of the group, M. amabilis. In the first data chapter of this thesis, I reconstructed the phylogeny of all four species of chestnut-shouldered fairy-wrens including all four subspecies of M. lamberti using a mitochondrial gene (ND2), five anonymous nuclear loci and three nuclear introns. Phylogenetic analysis of the mitochondrial ND2 gene nests M. amabilis within M. lamberti rendering the latter paraphyletic. Individual nuclear gene trees failed to reliably resolve each of the species boundaries or the phylogenetic relationships found in the mtDNA tree. When combined, a strongly supported overall topology was resolved supporting the monophyly of M. lamberti and its sister species relationships to M. amabilis. Current subspecies taxonomy of M. lamberti was not concordant with all evolutionary lineages of M. lamberti, nominotypical M. l. lamberti being the only subspecies recovered as a monophyletic group from mtDNA.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Historical changes to Australia’s climate have been proposed to have caused the decline of its ancient mesic biome. The fragmentation of habitat will affect species in different ways depending on their dispersal ability and their potential to disperse across inhospitable habitats. The diversification of Australia’s terrestrial species has been shown to have arisen due to climate changes that occurred during the Miocene – Pliocene, especially for those that occupy mesic habitats. Almost no comprehensive studies on freshwater insect groups from these habitats exist. In this thesis I investigate the role of past climate change on the evolution of a group that appear to be a specialist of the mesic zone, the Australian Psephenidae. I test two main hypotheses; first, that climate change during the Miocene has led to the diversification of the group, and second, that the limited dispersal capability of the beetle coupled with its habitat specialisation has led to further diversification within the genus. The molecular systematics and historical biogeography of the Australian Psephenidae was investigated using the mitochondrial DNA COI gene and the nuclear DNA H3 gene. Strong evidence for monophyly of the Australian endemic genus Sclerocyphon was found using three different tree building methods. The species tree revealed that the genus underwent a rapid divergence in the late Miocene, presumably as response to the fragmentation of their mesic habitat as Australia became increasingly arid. The timing of speciation within the Sclerocyphon coincides with other Australian freshwater taxa, and implies a vicariant explanation for the current distribution of the genus which is linked to the contraction of the mesic zone. Other vicariant events, such as the flooding of Bass Strait and the birth of Australia’s arid zone have also contributed to the current distribution patterns seen in the Sclerocyphon. More recent Pleistocene climatic events have resulted in further diversificati

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Australia’s largest and most important waterway- the Murray-Darling Basin (MDB) - is under threat owing to predicted increases in temperature extremes and reduction in rainfall - runoff in the coming decades. Management strategies are required that incorporate an understanding of dispersal patterns of the MDB fauna and flora. Patterns of dispersal have typically been studied through direct organismal studies but genetic approaches, in which the movement of genes in the landscape is used as a correlate of species dispersal, can provide a more comprehensive view by investigating at a much larger temporal and spatial scale. Genetic connectivity (dispersal) is influenced by the biology of the species, and by flow regime and the dendritic pattern of the network in riverine landscapes. An understanding of the relative influence of each on connectivity is required to deliver informed management strategies. Decisions regarding whether management for conservation is necessary also require an understanding of a species susceptibility to a changing environment. Species already exhibiting deleterious trajectories under current flow regimes in the basin may require more drastic measures than those that have remained unaffected.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Riverine environments present specific barriers and challenges to dispersing fish, depending on their dispersal capability. While some barriers are obvious and finite (for example a waterfall), the subtle influences of dendritic river network structure can also affect the dispersal, and therefore the genetic structure, of freshwater fish within river catchments. In addition to these natural barriers, artificial barriers like weirs and dams can have significant effects on the flow of genes between populations in rivers. In order to achieve the effective management and conservation of populations there is a need to understand dispersal and how the movement of individuals impacts populations at a variety of scales. Studies of dispersal are important for the perspective they bring to the movement and migration of individuals and the subsequent flow of genes – both temporally and geographically. It is this spread of genes that largely determines the genetic diversity of populations, which is a quality necessary for the stability and persistence of individuals and populations.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, This study investigated two protocols for use with taxonomic research and provides a significant step toward a comprehensive taxonomic revision of two Australo-Pacific snake genera: taipans (Elapidae: Oxyuranus) and brown snakes (Elapidae: Pseudonaja). These snakes are of interest to many people for reasons such as the proximity of their distribution to major urban centres, the potential lethality associated with their venom, and the morphological variation found in most sub-taxa. Distributed throughout Australia and parts of Indonesia and Papua New Guinea, taipans and brown snakes are noted both for their morphological variability and sub-taxa similarity. These two reasons are partially why, since the first species of brown snake was erected in 1854, 48 different (sub)species of Oxyuranus and Pseudonaja have been described as valid taxa. A third reason may be methodological: the use of inappropriate sampling techniques and laboratory methods. The present study tested and validated a novel systematic sampling methodology for taxonomic and systematic research, investigated the appropriateness for the inclusion of archival DNA in molecular research, and conducted phylogenetic and morphologic analyses of past and present data collected from these taxa. A review of the taxonomic history of these snakes (presented in Chapter 1) shows that the evolutionary relationships of Oxyuranus and Pseudonaja sub-taxa have long been uncertain. Previous taxonomic and systematic inquiries have been descriptive in nature, inconsistent characters have been selected for analysis, specimen selection has been opportunistic, and molecular studies have been reliant on fresh tissue for genetic analyses. These issues may be, in part, why there is still taxonomic uncertainty regarding the number of valid taxa associated with these snakes. This study attempted to uncover the evolutionary relationships of these snakes using novel and improved techniques. These techniques were first tested for thei

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Arts, Education and Law, Science, Environment, Engineering and Technology, Herbivory is one of the major ecosystem processes, as are pollination and seed dispersal, which drives ecological changes in both the phytophagous fauna and their host plant assemblages. The amount of herbivory damage on a host species represents not only the amount of herbivory pressure due to phytophagous insects but also the predatory pressure due to predators at higher trophic levels. Furthermore, additional interactions of climate and environmental factors determine the conditions of the host species and subsequently the assemblage of herbivorous insects that colonize them. All these direct and indirect, positive and negative influence of climate and environmental factors combined with the requirement to propagate themselves cascades to through the higher trophic levels down to assemblage of herbivorous insects and their host species at the lower trophic levels. This study considered the host specificity of caterpillars, herbivory pressure and herbivory damage on trees and shrubs along an altitudinal gradient within subtropical and temperate rainforest. The work has attempted to show how a selected ecological process (herbivory) is being influenced by various factors including altitude, ant predation pressure and host plant species, canopy strata and physical properties of leaves.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), CICS/School of Environment, Science, Environment, Engineering and Technology, Migratory shorebirds generally utilise very different habitats, great distances apart, during breeding and non-breeding seasons. The coastal intertidal flats in their non-breeding range provide a wide variety of benthic prey and shorebirds are primarily utilising these habitats for there foraging potential. Feeding strategies among shorebirds are largely determined by morphology and broadly range from visual pecking at the substrate surface to tactile probing deep within the sediment. Some shorebirds are capable of very deep (>15 cm) and complex probing of the sediment and this feeding guild is represented globally by three very large curlew species: Eastern Curlews (Numenius madagascariensis), Eurasian Curlews (N. arquata) and Long-billed Curlews (N. americanus). These deep-probing shorebirds are threatened globally due to recent declines in population sizes, largely resulting from habitat loss and hunting pressure. To prevent further loss and possible extinction of shorebirds at risk, better knowledge of their feeding ecology outside the breeding grounds is required. Moreton Bay on Australia’s subtropical east coast supports over 15% of the global population of Eastern Curlews during the austral summer months and is therefore of worldwide importance for this species during its non-breeding season. The present study investigates the feeding ecology of the Eastern Curlew in Moreton Bay and what drives their habitat choice on these nonbreeding grounds. Initially the broadscale distribution of Eastern Curlews among tidal flats within Moreton Bay was assessed. Low-tide surveys were conducted with the help of 60 skilled volunteers who made repeated counts at defined sections of tidal flat (sites) totalling approximately 41.3% (9,500 ha) of the intertidal habitat within Moreton Bay. Sites varied in size (0.68–474 ha), substrate, topography, and other features. There was a very high consistency between counts on different days within a month and different months within a

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, The fluctuating changes in climate during the Pleistocene period played an important role in population genetic structure of many species in northern and southern Australia. I investigated the population structure and history of a widespread Ross River Virus vector, the Australian saltmarsh mosquito (Aedes vigilax) across the continent. The main aim of this study was to determine levels of connectivity among sites across the continent. This information is important for disease control, because it can inform about the likely spread of pesticide resistance, as well as the scale at which control measures should be undertaken. In this study, the genetic structure of 379 individuals of this vector (Ae. vigilax) (Skuse) was examined and a comparative approach was taken in analysing patterns of genetic variation. The methods were mitochondrial COI sequence variation and nuclear variation at three microsatellite loci. Analysis of mitochondrial DNA data detected 119 haplotypes of which more than 50% were unique. Bayesian analysis revealed two distinctly divergent clades. Clade-I was only found in eastern Australia (Queensland and New South Wales), whereas Clade-II was found throughout the sampling area (Northern Territory, Western and eastern Australia). A molecular clock calibration was used to estimate the divergence time between the two clades to be 0.924 million years. The Nested Clade Analysis (NCA) indicated that there was significant geographical structure and suggested divergence between clade-I and clade-II by allopatric fragmentation. Increasing aridity during the Pleistocene was suggested as a factor in structuring Ae. vigilax populations. The Carpentarian barrier in the north was hypothesized to be associated with the divergence between the eastern and western clades. In addition, the Murchison arid barrier in the west could explain the low gene flow between south-western population (Perth site) and other western sites. A recent demographic expansion in the late

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Seagrasses are ephemeral, patchy habitats, under increasing risk of fragmentation due to anthropogenic changes. The ongoing and increasing loss of seagrass makes it essential that we understand the processes of movement and connectivity of the animals which rely on seagrass as a habitat. Shrimp are among the most abundant and diverse animals in seagrass habitats. Much of the published literature remains focused on one particular facet of shrimp life. Ecologists tend to generalise habitat-scale patterns of shrimp family groups where more specific studies on individual species may only focus on the biology, taxonomy or phylogeography alone. Few studies combine ecology, biology and phylogeography. This thesis attempts to achieve a comprehensive understanding of the biology, ecology, diversity, distribution, connectivity, and phylogeography of one of the most abundant shrimp taxa from Queensland seagrasses: Phycomenes zostericola. This holistic approach provides a solid foundation of information against which to compare future connectivity studies and also other seagrass species. In general, caridean shrimp are planktonic during their early life stages and will then recruit into the same habitat type which their parents occupy. Having a planktonic larval phase allows them the potential for broad dispersal. This study found that the potential for movement among P. zostericola populations is considerable; the adults were found to frequently move among seagrass patches and larvae have a planktonic phase of anywhere up to three weeks. Surprisingly, P. zostericola show a surprising amount of genetic structure for a marine species with a planktonic larval phase. The close association of adults to seagrass habitat and the reliance of P. zostericola larvae on a current to maintain suspension may be the limiting factors preventing P. zostericola from fulfilling their migration and dispersal potential. P. zostericola has a broad distribution and can be found in most seagrass habi

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Many species have been translocated from their native habitat into new environments. Some of these transfers have had negative impacts on the resident populations. Hybridization and introgression are some of the impacts that are associated with species incursions. These processes can potentially result in successful invasions and jeopardize the existence of native species and populations. It is thought that intraspecific hybridization can result in the loss of local adaptations and decrease adaptive divergence among populations. Understanding the factors affecting survival of the native species in altered landscapes is an important issue in species conservation. This study explores the processes that could lead to asymmetrical hybridization between two closely related lineages of freshwater shrimp Paratya australiensis. Selection pressure appears to be leading to extinction of one lineage in most of the sites adjacent to a pool where a translocation resulted in mixing of the two lineages (Hughes 2003). The aim of the thesis was to identify the processes and traits involved in the shaping of the current genetic structure of this shrimp following the translocation event; using genetic markers to identify what could have triggered the asymmetrical hybridization and almost complete extinction of the resident lineage. This is an ideal model system to study and understand interactions between recently (2-3 million years ago) diverged lineages. The translocated lineage 4 comes from Kilcoy Creek, which is at a higher altitude (cold temperatures) than Stony Creek, where the resident lineage 6 is situated (warm temperatures). The temperature differences and the fact that the two lineages were thought to have been isolated for 3million years, led to the expectation of some degree of reproductive isolation. Hughes et al. (2003) found that, after this translocation the reproductive isolation was asymmetrical, such that most of the males appeared to mate only with females from th

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment, Science, Environment, Engineering and Technology, Ecological theory and research has shown a critical link between in-stream connectivity and the ecological persistence of aquatic fauna with particular emphasis on taxa with higher commercial or recreational value such as fishes. However, limited information exists on both the dispersal levels and behaviour of fish that have no obvious economic or conservation values. The biological connectivity (or isolation) of individuals/populations across heterogeneous spatio-temporal dimensions occurs primarily via the processes of movement and dispersal. The movement of individuals affects current patterns of population dynamics over an ecological timescale whilst dispersal ultimately shapes the level of gene flow among populations and contributes to the processes that shape population dynamics over an evolutionary timescale. Despite the temporal differences in scale, both the ecological and evolutionary outcomes of connectivity are governed by the ability of individuals to freely move or disperse through all axes of space and time. This very ability for individual connectivity relies on factors both intrinsic and extrinsic to the species. In an attempt to better understand the fundamental population dynamics of aquatic fauna in the natural environment, it is vital to design and apply methodologies that can accurately estimate in-stream levels of connectivity. By utilising such techniques researchers can then determine the underlying biological principles that shape the patterns of distribution and abundance for a given species and use these key biological indicators to contribute to the information required in the long term protection and management of an often undervalued resource. The focus of the study was to estimate levels of connectivity in a model species, the ubiquitous Australian smelt (Retropinna semoni), both on an ecological and an evolutionary timescale across contrasting drainage systems from inland rivers of Australia. Contrasting patterns of connectivity from

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Science, Environment, Engineering and Technology, Historically, when the terms “conservation, threatened, endangered or extinct” were used, it was in reference to vertebrate animal species. Funding for conservation and policy implementation for protection of invertebrates has historically been difficult, even though 95% of all animal species are invertebrates and are an important component of many ecosystems. Human impact on the earth has influenced the natural population structure of many organisms, through habitat destruction, fragmentation and degradation. Issues that affect population structure and dispersal are heightened when that species is confined to a specific range or habitat. This is especially paramount for aquatic organisms with the slightest change in weather pattern, damage to riparian zones or the stream environment, or alteration to stream engineering and water flow resulting in significant impacts to the stream biota. Freshwater mussels are organisms that have been found to be seriously affected by changes to stream conditions. Because mussels filter the water column, they are generally the first group of animals to react if contaminants enter a system and as a result freshwater mussels are considered by many scientific and government agencies worldwide as key indicator species for stream health assessments. Freshwater mussel conservation is a relatively unexplored field within Australia and little is known about mussel recruitment and patterns of population connectivity. Mussel taxonomy in Australia is based entirely on shell morphology, although local environmental conditions have been shown to have significant effects on shell morphology. Therefore, basing taxonomy purely on shell morphological characteristics may not to be systematically meaningful. Before effective conservation measures can be implemented within Australia, clarification of contemporary mussel diversity is required.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment, Science, Environment, Engineering and Technology, Many of Bactrocera are of particular concern throughout much of Asia and the Pacific, where they constitute a significant threat to agricultural production. Bactrocera cacuminata is a native and non-pest species in Australia, which can be used as a model species for studies of pest Bactrocera flies. Over the past four to five decades, knowledge of the ecology and biology of Bactrocera has been established based mostly on laboratory and semi field conditions. The behavioural strategies of Bactrocera have been broadly hypothesised as (1) females mate mainly only once; (2) adults emerging from a fruit will be full sibs, i.e. members of the same family; (3) there is genetic differentiation between regions but not between sites within regions and there is an overall pattern of IBD. Understanding aspects of the behaviour of Bactrocera flies is important for providing a context for other avenues of investigation including studies on pest management. The objective of this study was to use molecular techniques to test the hypotheses above in wild B. cacuminata. Specifically the aims were: 1) to estimate the level of polyandry, sperm utilization and sperm selection by analysing offspring genotypes from wild-caught females, 2) to estimate patterns of oviposition and larval development by analysing genotypes of flies emerging from wild fruit, 3) to estimate patterns of dispersal between populations on different spatial scales, within/between region(s). Estimates of gene flow (derived from hierarchical population genetic variation analyses) were used to infer patterns of dispersal. For this study, six polymorphic microsatellite loci and mtDNA gene, ND4 were developed. The microsatellites were isolated from enriched genomic libraries constructed using a biotin/streptavidin capture protocol. Allele number varied between three and nine; the expected heterozygosity ranged between 0.29 and 0.81. No significant deviations from Hardy–Weinberg equilibrium or linkage disequilibrium were

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment, Science, Environment, Engineering and Technology, Understanding patterns of dispersal, the movement of individuals or propagules, among populations of riverine species is imperative to their management and conservation. However, directly estimating dispersal can often be difficult. Therefore, estimates of gene flow, the movement of genes, are often used to infer dispersal among natural populations. In riverine species, gene flow is determined by species biology, riverine architecture and flow regime. While many studies investigate the role of species dispersive strategies by comparing patterns of genetic structure in different species across the same geographic range, few also attempt to investigate the role of the non-biotic influences on gene flow in a comparative manner. Instead, studies regarding landscape processes (river architecture and hydrology) are based upon observations in a single riverine environment and not compared to other catchments that may differ in riverine architecture or hydrology. This study attempts to investigate all three factors influencing gene flow and genetic diversity using a comparative approach. This is done by contrasting two species of freshwater fish in two riverine systems that differ in their hydrological and structural makeup. By comparing patterns of genetic structure for each fish species, the role of species biology (behavioural and physical adaptations) can be explored. Then, by comparing patterns of genetic structure for each species, between riverine systems that differ in their landscape processes, the role of hydrology and riverine architecture in determining genetic structure can be explored. This study employed three different genetic markers to elucidate patterns of genetic structure and genetic diversity. These were, direct sequencing and screening of the control region of the mitochondrial DNA genome, microsatellite loci and allozymes...

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean gener

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, Science, Environment, Engineering and Technology, Phosphorous (P) and nitrogen (N) are the most dynamic and often growth-limiting plant nutrients in terrestrial ecosystems because of their nutritional and physiological significance. In this study I address one of the most important functions of roots, the uptake of nutrients and their distribution throughout plant tissues. The fundamental mechanism involved in these processes is the transport of mineral nutrients that are charged across lipid membranes. The use of molecular tools by nutritional physiologists over the past decade has resulted in the identification and characterisation of genes that encode the transporter proteins from a number of crop plant species. Most of the molecular nutrient studies have targeted crop species, with very limited studies on tree species like Hoop pine. I was unable to amplify cDNA sequences encoding ammonium transporter genes from Hoop pine cDNA after genomic and cDNA screening with primers related to known ammonium transporters. No sequences similar to ammonium transporter sequence in Arabidopsis thaliana AtAMT1;1 was found in Hoop pine using Southern Blot analysis where AtAMT1:1 was used as a probe. This suggests that the large evolutionary distance between Angiosperms and Gymnosperms may be the reason behind the difference between AMT sequences in Hoop pine trees and AMT in other Angiosperm species used in designing the primers which have been used in PCR and RT-PCR. The same reason may be behind not getting ammonium transporters in Hoop pine trees related to AtAMT1;1 in Arabidopsis using Southern Blot or PCR techniques The other possible explanation is the mycorrhizal associations and root adaptations which may enhance the ability to substantially broaden the N source base for Hoop pine trees. The role of mycorrhiza in N uptake in Hoop pine needs to be further investigated. The strategy of using genomic DNA, not only the root cDNA as in most of studies on phosphate transporters (Pht), led to the identification of phosphate tr

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, Faculty of Environmental Sciences, Connectivity in ecological systems is a broad concept that embodies the transmission of ecosystem components throughout landscapes at multiple spatial and temporal scales. Of relevance to the present study are the connections (or lack thereof) among local populations of stream fauna - population connectivity in lotic systems. Dispersal, recolonisation and migration are the demographic forms of population connectivity, and gene flow is the genetic aspect of population connectivity. Both forms of population connectivity have underpinned some of the classic theories and hypotheses in stream ecology, and have implications for pure and applied stream ecology, including ecosystem restoration. Conceptual models in ecology can facilitate understanding and predictability of the ecosystem processes they represent, and have potential applicability as management tools or 'rules of thumb' in conservation and restoration programs. Various theoretical models describe potential patterns of connectivity among local populations and in this thesis these models were used to evaluate population connectivity in a freshwater fish (southern pygmy perch, Nannoperca australis) and two reproductively isolated genetic lineages of freshwater shrimp (Paratya spp.) in small, geomorphically degraded streams in south eastern Australia. These streams (the Granite Creeks) have been the focus of a recent habitat restoration trial and several studies have examined fish and macroinvertebrate community responses to the experiment. It was the purpose of this study to contribute information about population connectivity in the selected species to complement these community ecology studies. Population connectivity was examined in these species using molecular data (mitochondrial and nuclear genetic data) and natural abundance isotopic signatures of nitrogen and carbon. At the landscape scale, results showed that populations of N. australis and the P. australiensis lineages were isolated among the streams an

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environmental Studies, Science, Environment, Engineering and Technology, Freshwater species are expected to show higher levels of genetic structuring than those inhabiting estuarine or marine environments because it is difficult for freshwater species to move between river systems. However, freshwater species that exhibit some tolerance to salt water may be capable of marine dispersal and therefore may show lower levels of genetic structuring. The species that are restricted to freshwater are likely to have genetic structures that reflect the history of those drainages. Various studies have attempted to use genetic data to infer past geomorphological changes. For example, stream rearrangements were thought to have influenced the distribution of genetic diversity in the purple spotted Gudgeon, Morgunda morgunda (Hurwood and Hughes, 1998). The main aim of this study was to resolve the relative significance of contemporary and historical events in structuring populations of freshwater species in southeast Queensland river systems. The study revolved around four freshwater species namely the ornate rainbow fish Rhadinocentrus ornatus, the empire gudgeon Hypseleotris compressa, the endemic freshwater shrimp Macrobrachium australiense and freshwater shrimp Macrobrachium tolmerum, and examined patterns of genetic variation using allozyme and mtDNA analysis and also previously established hypotheses of biogeographic association among these regions was tested. It was hypothesized that R. ornatus and M. australiense, which are restricted to freshwater, would display genetic structure similar to the species which had already been examined i.e., would show similarities among streams along the Sunshine Coast region only (Hughes et al., 1999), because these creeks were thought to have had a confluence before they reached the sea, during the last 10, 000 BP. The results for R. ornatus and M. australiense, were different from expectations, In contrast to earlier studies, there was evidence of restricted gene flow among sites within the Sunshine Coast re

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environmental Science, Science, Environment, Engineering and Technology, This study investigated spatial genetic structuring of two groups of Australian Ogyris butterflies (Lycaenidae). Ogyris represents one of several Australian endemic butterfly radiations that is well characterised in terms of basic biology but lacking in data useful for discriminating among the potential factors promoting divergence and speciation. A phylogeographic approach was used to document structuring in mitochondrial DNA markers (mtDNA) across the geographic range of two groups of closely related taxa. These include a pair of sister species: Ogyris zosine and O. genoveva, and the polytypic species O. amaryllis which is comprised of four subspecies. Topological relationships among recognised taxonomic units were tested and polyphyletic patterns investigated as a potential source of information relating to divergence and speciation. Sister species Ogyris zosine and O. genoveva were found to exhibit a polyphyletic relationship based on mtDNA. The deepest divergence within the group separated allopatric populations of O. zosine in northern Australia which do not correspond to a recognised taxonomic entity. The distribution of O. zosine and O. genoveva is parapatric along the east coast and additional sampling in this area along with evidence from allozyme markers revealed that the polyphyletic pattern can be explained by past mtDNA introgression at the current contact zone. The two species engage in an obligate mutualistic association with different suites of Camponotus ant species. It is hypothesised that this association may be involved in maintaining differentiation between the taxa through ant-mediated selection against hybrids. The distribution of a blue/purple wing colour polymorphism in female O. zosine is consistent with the role of wing colour as a prezygotic isolating mechanism in the contact zone although other explanations cannot be excluded. Genetic relationships were examined among four nominal taxa of the polytypic species Ogyris amaryllis which hav

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Environment, Faculty of Science, Environment, Engineering and Technology, An increasing number of endangered species have reached the threshold prompting management decisions to commence captive breeding and reintroduction. Such intervention is costly and requires a substantial investment of resources that might otherwise be spent on alternate conservation options. It is important, therefore, that such measures make use of all available information to ensure the success of the reintroduction effort, not just in the short-term but also well into the future. The diverse range of elements to be considered include habitat factors, number and sex ratio of founders, number of populations to establish, source populations to use, timing of releases and the need to supplement the populations. All of these factors can benefit through input from molecular genetic data to improve the quality of information used in decision making. Levels of genetic variation are strongly correlated with population fitness and their potential for long-term persistence. For this thesis I examined levels of genetic diversity at neutral and functional regions of the genome for two endangered species of Australian marsupials: the western barred bandicoot, Perameles bougainville; and Queensland populations of the greater bilby, Macrotis lagotis. These two species are under threat from similar processes: habitat destruction and modification for agriculture; predation by foxes and feral cats; changes to traditional fire regimes and competition with introduced pest species. Since European settlement, P. bougainville has become extinct on the mainland and now exists on just two islands in Shark Bay, Western Australia. Macrotis lagotis has suffered a range contraction of over 80% and the Queensland population has become disjointed from other populations to the west. Reintroduction efforts are under way for both species but, until now, the projects have not made use of molecular genetic data to inform their management decisions. I have used marker systems from nuclear microsatel

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, Faculty of Environmental Studies, During the Pleistocene, fluctuating climates led to cycles of glacial/arid activity interspersed with pluvial periods across continents in both northern and southern hemispheres. Many studies in the northern hemisphere have used genetic analysis to document the important role that glacial activity has played in structuring avian populations at high latitudes. However, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. I investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen) and two species of obligate feather ectoparasites. 1166 samples from across the native range of G. tibicen were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. Analysis of mitochondrial variation at the sites sampled in this study suggested the contemporary distribution of eastern and western clades is non-overlapping but in close proximity. Analysis of microsatellite variation suggested that secondary contact may have occurred between eastern and western clades in north-western Australia. From AMOVA analysis and Bayesian analysis of population structure (BAPS) it was indicated that contemporary nuclear gene flow preceded mitochondrial gene flow from eastern populations through to north-western Australia. Most eastern, northern and north-western sites showed little geographic structure for microsatellite variation. BAPS analysis of microsatellite variation however, suggested there was as much structure among south-west populations as there was between eastern and western populations. For a majority of population comparisons, estimates of gene flow based on coalescent analyses (LAMARC) s

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, The butterfly family Lycaenidae (including the Riodinidae) contains an estimated 30% of all butterfly species and exhibits a diverse array of life history strategies. The early stages of most lycaenids associate with ants to varying degrees, ranging from casual facultative coexistence through to obligate association where the long-term survival of the butterfly is dependent on the presence of its attendant ants. Attendant ants guard the butterflies against predators and parasites during their vulnerable period of larval growth and pupation. The caterpillars, in return, reward the ants by providing attractive secretions from specialized glands in their cuticle. The prevalence of caterpillar-ant associations in the species rich Lycaenidae is in contrast with other Lepidoptera, where ant association appears only as isolated cases in otherwise non ant-associated lineages. This has led to the proposal that ant association may have influenced lycaenid diversification or even enhanced the rates of speciation in the group. In contrast, facultative ant-associated butterflies exhibit high levels of host plant integrity, so it is reasonable to assume that host plants may have played a significant role in their diversification. Since the influence of ants (or plants) on diversification is independent of geographic speciation modes such as vicariance or peripheral isolates, there is an underlying inference of sympatric speciation. Certain prerequisites thought to be important for sympatric speciation, such as mating on the host plant (or in the presence of the appropriate ant) as well as ant dependent oviposition preferences are characteristic of many obligate myrmecophiles. Not surprisingly, it has been suggested that evidence for sympatric speciation is more likely to be found in the Insecta since this additional mode of diversification could account for the large numbers of insect species. This thesis tested the diversification processes in obligate and facultative ant associ

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, Soil microorganisms play important roles in maintaining soil quality and ecosystem health. Development of effective methods for studying the composition, diversity, and behavior of microorganisms in soil habitats is essential for a broader understanding of soil quality. Forest management strategies and practices are of vital significance for sustainable forest production. How the different forest management measures will influence soil microbial communities is a widespread concern of forest industry and scientific communities. Only a small proportion (~0.1%) of the bacteria from natural habitats can be cultured on laboratory growth media. Direct extraction of whole-community DNA from soil, followed by polymerase chain reaction (PCR) and other analysis circumvents the problems of the culture-dependent methods and may shed light on a broader range of microbial communities in the soil. DNA-based molecular methods rely on high quality soil microbial DNA as template, and thus extraction of good quality DNA from soil samples has been a challenge because of the complex and heterogeneous nature of the soil matrix. The objectives of this research were to establish a set of DNA-based molecular methods and to apply them to investigate forest soil microbial composition and diversity. Soil samples were collected from different forest ecosystems, i.e., the natural forest (YNF) and the first rotation (~ 50 years) (Y1R) and the second rotation (~ 1 year) (Y2R) of hoop pine plantations at Yarraman, and from different forest residue management practices (the experiments had established 6.4 years before the samples were collected) at Gympie, two long-term experimental sites of the Queensland Department of Primary Industry-Forestry in subtropical Queensland, Australia. Some DNA-based molecular techniques, including DNA extraction and purification, PCR amplification, DNA screening, cloning, sequencing and phylogenetic analyses, were explored using Yarraman soil samples, which were high

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, Arid and semiarid river systems in Western Queensland, Australia, are characterized by the unpredictable and highly variable nature of their hydrological regimes as a result of the episodic nature of rain events in the region. These dryland rivers typically experience episodic floods and extremely low or no flow periods. During low or no flow periods, water persists only in relatively wide and deep sections of the river channels, which are called 'waterholes'. These isolated waterholes serve as refugia for aquatic species during protracted intervals between floods. In such discontinuous riverine habitat, dispersal of freshwater species may be achieved only during wet seasons, when water is flowing in rivers and the nearby floodplains. Obligate aquatic species occur in habitats that represent discrete sites surrounded by inhospitable terrestrial landscapes. Thus, movements are very much limited by the physical nature and arrangement of the riverine system. In addition, the distribution of a species may be also largely dependent on historical events. Landscape and river courses continually change over geological time, often leaving distinct phylogenetic 'signatures', useful in reconciling species' biology with population connectivity and earth history. The main aim of this study was to resolve the relative importance of contemporary and historical processes in structuring populations of two freshwater species in Western Queensland river systems. To address this aim, a comparative approach was taken in analysing patterns of genetic variation of two freshwater invertebrates: a snail (Notopala sublineata) and a prawn (Macrobrachium australiense). Mitochondrial sequences were used for both the species. In addition, allozyme and microsatellites markers were employed for N. sublineata. These species have similar distributions in Western Queensland region, although N. sublineata appears to be extinct in some catchments. M. australiense is thought to have good dispersal abili

Full Text, Thesis (Masters), Master of Philosophy (MPhil), Australian School of Environmental Studies, This study investigated the utility to vertebrates of upland linear riparian rainforest fragments on the Atherton and Evelyn Tablelands in the Australian Wet Tropics region, north Queensland. Similar linear fragments were selected, that varied in forest age and their connectivity to large areas of continuous forest:- (connected primary (N=6), isolated primary (N=5), connected secondary (N=6) and isolated secondary (N=7)). Primary sites had either never been cleared or only subject to selective logging, while secondary forest had been completely cleared and allowed to regenerate for at least 30 years. These linear fragments were contrasted with riparian sites within continuous forest sites (N=6 to 7), which were situated in State Forest or National Parks, and sites within the cleared matrix (pasture, N=6). Vertebrates surveyed were birds, ground-dwelling mammals and reptiles, particularly leaf-litter skinks. All surveys were conducted between September and December in 2001 and/or 2000. Chapter 2 investigates the effects of forest age, isolation and structural vegetation features on bird assemblages within linear riparian fragments of rainforest. Bird surveys and structural vegetation assessments were conducted within connected and isolated primary and secondary linear fragments, and compared with those of continuous forest habitat (N=6) and pasture. There were strong effects of forest age; all three types of primary rainforest had higher values than secondary rainforest for most measured attributes of vegetation structure (including canopy height and cover; and frequency of large-diameter trees, lianes, epiphytes, strangler figs; and woody debris), but lower frequencies of tree ferns and thorny scramblers. Sites within primary rainforest also had a greater frequency of many bird species across different guilds of habitat, feeding and movement. Assemblages of rainforest-dependent birds showed an effect of isolation, although its strength was less than that of forest a

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, The White-bellied Sea-Eagle Haliaeetus leucogaster is widespread in Australia, but has been the subject of conservation concern due to suggested localised declines and extinctions. Regionalised monitoring programmes have addressed some aspects of local concern, however a broader approach is needed to gain an understanding of large-scale processes affecting long-term persistence at scales equivalent to the species Australian range. Ultimately, the ability to predict change in population size over time accurately depends on the scale of analysis. By necessity, ecological studies using direct sampling techniques are often made across spatial scales smaller than a species geographic range and across relatively short time frames. This seems counter-intuitive considering that long-term species persistence is often dependent on large-scale processes. The principal aim of this thesis was to identify historical and contemporary forces responsible for the current pattern of population structure in H. leucogaster. This required a multi-scale approach, and the resulting research uses genetic, distributional and morphometric data. Haliaeetus leucogaster is a large territorial raptor that historically has been associated with coastal regions, lakes and perennial river systems. It has an extensive worldwide distribution from the western coast of India throughout the Indomalaysian region, Papua New Guinea and Australia. By virtue of the species' large-scale distribution, in Australia it is fairly cosmopolitan in its use of habitat and prey types. Haliaeetus leucogaster is monomorphic for adult plumage colouration, but in body size displays reversed sexual dimorphism with female birds significantly larger. A discriminant function based on 10 morphometric characters was 100% effective in discriminating between 19 males and 18 females that had been sexed using molecular genetic methods. Re-classification using a jackknife procedure correctly identified 92% of individuals. The discrimi

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, The Australian magpie (Gymnorhina tibicen) is a large, sedentary, omnivorous passerine. In some populations, individuals live in groups, and some of these groups breed cooperatively. The white-backed magpie (G. t. tyrannica) from the south-eastern corner of the continent, has had relatively little study, and few details are known of its mating system, social structure, and method of parental care. I conducted an observational study on a population of white-backed magpies, recording details of their demography, dispersal, breeding system, and parental care. In conjunction, I conducted a genetic analysis of the population, to determine if the genetic mating system matched the observed social system, to detect instances of extra-group mating, and to sex juvenile birds. Extra-pair paternity (EPP) is a common feature of the mating systems of many birds. The rate of EPP may vary between species, races and populations. I made a comparison of extra-group paternity (EGP) rates between two races of the Australian magpie, to determine if similar mating systems were being employed. The two populations had similar social structure, but differed in group size and dispersal. I predicted that dispersal differences would have a profound effect on the rate of EGP between the populations, as the population with the lower rate of dispersal and higher chance of breeding with a close relative would engage in EGPs more frequently. Eight microsatellite loci were used to determine parentage in the white-backed Australian magpie. The rate of EGP was found to be 44%. Dispersal rates were estimated from observational data. Over half of the juvenile magpie cohort from the previous breeding season leave the territorial group. These results contrast sharply with the results found by other researchers in a population of western Australian magpies (G t. dorsalis). In this population, 82% EGP is recorded and dispersal of juveniles is close to nil. The results indicate that dispersal rate is a potent

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, The urbanised environment provides ecologists with unique situations in which to undertake ecological study. It has been said that urbanisation is like a natural experiment; we often have populations of animals that have gone from living in natural or semi-natural environments to living in a highly modified anthropogenic environment. These situations provide ideal settings to study the ecological and behavioural differences that may develop in populations located in different habitats. Urbanisation typically results in a minority of species dominating the fauna, and this thesis aimed to examine one such species, the Australian magpie. Despite the magpie being a common and well-liked suburban bird, the majority of previous research on this species has been undertaken within rural or exurban locations. This thesis aimed to examine what actually happens to the species when it lives in the suburban environment. In particular I focused on specific behavioural and ecological features, to see if there were any particular adaptations the suburban magpies showed and also if the suburban habitats provide certain resources favourable to the magpies and what ecological effects these may have. Comparisons of the territory structure and resources of rural and suburban magpies showed that although many features of the territory are similar between rural and suburban locations, notably the choice of native nest trees, magpie territories within suburban areas were smaller and contained more anthropogenic features. The reduced territory size may possibly be related to a greater abundance of key food resources also evident within suburban areas. Furthermore, suburban magpies are more successful in their foraging attempts, again possibly reflecting a more abundant food supply in suburbia and also the simplified nature of suburban foraging areas might facilitate more successful foraging. The increased foraging success is likely to explain the greater provisioning rate to nestling suburb

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, In this study, the relative influences of selection, gene flow, and other evolutionary forces on the spatial structure of genetic variation within a eucalypt species complex (the spotted gums: genus Corymbia, section Politaria) were assessed. The study investigated the spatial genetic structure among four putative species of spotted gum (broad-scale), as well as within a single population (fine-scale)of one species, using both molecular and quantitative markers. The spotted gum complex occurs naturally across a range of 2500 km in eastern Australia. Spatial genetic variation within and between the four putative spotted gum species was examined using both chloroplast and nuclear markers. No significant differentiation was found between the three northern species of the complex, C. citriodora, C. variegata and C. henryi. The southern species, C. maculata, shared no haplotypes with any of the three northern species. These results disagree in part with those reported in a previous allozyme based study in which C. henryi was found to be significantly divergent from C. variegata (with which it is sympatric) and more closely aligned with C. maculata. Re-analysis of the allozyme data provided evidence of selection acting at the PGM2 locus within populations of C. variegata and C. henryi. The exclusion of this locus from the data set led to concordance between the cpDNA and nDNA analyses. Restricted gene flow and evidence of isolation by distance were identified as the dominant processes influencing the contemporary distribution of the cpDNA haplotypes. No geographic structure of haplotypes was found and complex genealogical relationships between haplotypes indicated the combined effects of past fragmentation, range expansion and possible long distance dispersal events. The variation and spatial structure in both neutral molecular markers and quantitative genetic traits were compared to explore the relative influences of dispersal and selection within a single eucalypt popul

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Australian School of Environmental Studies, Two eucalypt clines were examined using morphological, ecophysiological and molecular analyses. The species complexes examined were an ironbark complex (Eucalyptus melanophloia x E. whitei) and a box complex (E. brownii x E. populnea). Both of these complexes demonstrate continuous morphological variation across their clines. The origin of these morphological clines has previously been interpreted as the product of secondary contact between allopatric species. In this study, an analysis of morphological variation across the clines did not identify an increase in trait variance in the intermediate populations, which suggests that previous theories concerning the origin of these clines may not be valid. Genetic structuring in nuclear and chloroplast DNA was examined across the clines to investigate whether the morphological clines were the product of secondary contact between two independent evolutionary lineages, or whether the clines represent a single evolutionary lineage that has undergone primary differentiation. The microsatellite analyses indicated that there was little genetic structuring across either cline, and that there were only low levels of population differentiation. The lack of hierarchical structuring in the distribution of nuclear genetic variation suggests that these clines are unlikely to be the product of recent gene flow between two formerly allopatric species/populations. A nested clade analysis of the JLA+ region of the cpDNA provides additional evidence to reject the null hypothesis that the morphospecies classifications represent distinct evolutionary lineages. Instead the analyses indicate that each cline represents a single cohesion species and a single evolutionary lineage. The phylogeographic distribution of cpDNA haplotypes is likely to have resulted from restricted seed mediated gene flow with isolation by distance. A more cogent explanation for the clines, based on the genetic data, is that they have arisen through the process of cont