Zoology - Theses
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ItemUnderstanding how climate affects the koala, Phascolarctos cinereus: the roles of behaviour, morphology and physiology( 2013)Understanding why species live where they do and not elsewhere, and what it is about their traits or the properties of their environment that has led to this distribution, is one of the fundamental aims of ecology. The role of climate in setting species distribution limits has become a topic of much research in recent times, as ecologists seek to predict how species’ ranges may expand, shift, or contract under future climate change. How climate influences species is mediated by the physiology, morphology and behaviour of individuals and how these interact with each other and the local environment. Understanding how climate limits species distribution therefore requires an approach that accounts for both exposure to climate (as mediated by behaviour, local climate and habitat features) and sensitivity (as influenced by physiological and morphological traits). Mechanistic models of species distributions aim to explicitly capture the links between the functional traits of organisms and their environments, based on the principles of biophysical ecology. For broadly distributed species, both the exposure and sensitivity of individuals to climate can vary substantially across their geographic range, along with the processes and key traits that determine the species’ range limits. In this thesis I investigate how climate influences the energy and water requirements of a broadly distributed arboreal marsupial: the koala, Phascolarctos cinereus. I focus particularly on how behaviour and morphological variation mediate the effect of climate on koalas. To evaluate whether koalas use behaviour to buffer themselves against variation in climate I collected microclimate data and behavioural observations of koalas under a range of environmental conditions at sites near the northern (Magnetic Island) and southern (French Island) edges of their geographic range. Using museum specimens I also quantified variation in two key morphological traits that influence heat exchange – fur depth and body size. Data on koala behaviour, morphology and physiology were incorporated into a mechanistic model that predicts energy and water requirements of koalas with different behavioural and morphological traits, exposed to different environments. To test the model, I measured energy and water turnover of free-ranging koalas at both Magnetic Island and French Island over summer using the doubly-labelled water technique. Using this model, I was able to quantify the importance of behavioural and morphological variation in koalas, and how these traits interact with each other and the local environment to influence energy and water requirements. By coupling the models with spatial climate datasets I was able to predict daily energy and water requirements of koalas across the Australian landscape for the last 20 years. This modelling approach is unique in its capacity to identify key processes limiting the current distribution of this species, and to predict responses to future climate change.
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ItemFire, foxes and foliage: conservation management of the southern brown bandicoot and long-nosed potoroo( 2013)Many regions around the world continue to experience faunal declines, despite the global recognition of the need to reduce the current rate of biodiversity loss. Disturbance events can contribute to such biodiversity loss, by disrupting the structure and function of populations, communities and ecosystems, threatening their ongoing viability by changing the availability of key resources. Fire and introduced predators are two disturbances that occur in many places around the world, and are particularly prevalent in Australia. These disturbances interact with each other, and also influence habitat suitability for fauna. Threatened species recovery therefore requires an understanding of the threats that affect species, and the implementation of evidence-based conservation management. The aim of this thesis is to identify the habitat characteristics and land management practices essential for the ongoing survival of the long-nosed potoroo, Potorous tridactylus, and southern brown bandicoot, Isoodon obesulus, in the context of fire and predator control. Uncertainty, variability and conflicting land use and management objectives can make effective land management challenging. By undertaking environmental management actions designed as experiments we can gain new information, and tease apart multiple management effects. Using an existing experimental framework of sites stratified into those treated with red fox (Vulpes vulpes) control and those not, overlayed on fire history data, we characterise the habitat of the long-nosed potoroo and southern brown bandicoot in far south-west Victoria. Our results suggest that potoroos were more likely to occupy Heathy Woodland and Mosaic EVC sites, though further habitat preferences could not be identified. Despite our efforts to provide more robust results through an experimental framework, we were unable to identify habitat features which clearly determined the presence or absence of bandicoots. These results highlight the inherent difficulties in determining habitat associations of low density, threatened species. Camera traps are increasingly used to monitor wildlife. Traditionally set aimed horizontally towards a scent lure, a vertical camera orientation is also being used, whereby the camera lens and sensor face vertically down towards the scent lure, capturing images from above. We aimed to compare detection probabilities of southern brown bandicoots and long-nosed potoroos by camera traps set horizontally, to those set vertically. Detection probabilities for both species were two to five times higher by vertical compared to horizontal cameras, with no significant difference in false triggers. Vertical camera orientation is shown to be superior in our study system, providing a valid alternative method to horizontal camera orientation. Fire is a disturbance that occurs naturally, but is also used as an ecosystem management tool through the application of planned burns. Long-nosed potoroos and southern brown bandicoots are potentially threatened by inappropriate fire regimes resulting from the suppression and application of fire in the environment. Understanding how these species are affected by fire is important for ongoing conservation and fire management. We use vertical camera traps to monitor potoroos and bandicoots before and after an experimental planned burn in south-west Victoria, Australia. Using a multi-season occupancy modelling approach we investigate the processes governing the probability of local extinction and colonisation of the two species after fire. Both species experienced high probabilities of extinction, and low probabilities of colonisation for up to 18-months post-fire. Potoroos and bandicoots appear to be responding to changes in essential resources in different ways. Whilst potoroos made use of unburnt vegetation patches, with extinction and colonisation probabilities post-fire linked to the presence of these patches, bandicoots did not. This study shows the differential responses of potoroos and bandicoots to a planned burn, and highlights the importance of understanding species-specific responses to fire. The availability of suitable refuges during and after a disturbance event contributes to the ability of fauna to survive. Fire is a key disturbance process, but does not burn in a homogeneous manner, so refuges can be created in the form of unburnt vegetation patches. We investigate the use of such refuges by the long-nosed potoroo. We monitored the survival and behaviour of individuals immediately after the fire, and then again at 16 months after fire, focussing on their use of unburnt patches compared to the burnt matrix for nesting and foraging. Unburnt refuges of intact vegetation apparently provided essential post-fire habitat for long-nosed potoroos. Unburnt vegetation patches were used exclusively for nesting by potoroos, at least up to16 months after fire. During active foraging times potoroos used unburnt patches more than 45% of the time. We suggest these unburnt patches functioned as refuges by providing key resources (e.g. appropriate nesting sites, protection from predators) to allow ongoing survival. A number of management recommendations have been made in response to the findings of this thesis. These recommendations address the two key threats to the southern brown bandicoot and long-nosed potoroo, of inappropriate fire regimes and predation by the red fox. They are informed by evidence from results presented in this thesis together with existing scientific knowledge of the two species. If implemented as part of an adaptive management framework as proposed, these actions can be further assessed, reducing uncertainty into the future.
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ItemThe regulation and development of the marsupial appendage( 2013)The mammalian appendage is extremely diverse and complex none more diverse than the limb and phallus. These two seemingly unrelated appendages share many similarities particularly in their development and patterning. The parallels between the development of the two appendages are remarkable but there are some key differences between the two structures. The mouse model is predominantly used to investigate these pathways but alternative models which possess specialised traits and morphologies have helped to uncover new pathways involved in the development and evolution of these appendages. In particular, the tammar’s mode of reproduction and it specialised limbs have provided new avenues for investigation of the key mechanisms of development and evolution of the limb and phallus. The cellular, molecular and hormonal changes that that occur in the developing marsupial during limb and phallus formation are described in this thesis. Here, this study focussed on the macropodid marsupial limb, which demonstrates one of the most dramatic examples of heterochrony, which can be defined as the difference in developmental timing between the fore and hind-limb. Heterochrony is clearly evident across all marsupial species to varying degrees. In the tammar, I find that there was high conservation of gene function but clear differences in the timing and mechanism of heterochrony when compared to the only other marsupial species so far examined, the opossum. The heterochrony between the macropodid fore and hind-limb is achieved through a minor shift in the induction of the forelimb marked by TBX5 expression and a later acceleration of downstream growth and patterning elements as compared to the mouse. In contrast, the opossum heterochrony, in which the entire limb patterning program starting from induction of the limb bud was shifted forward in time, began much earlier compared to that of the tammar. In addition, there was variability in the physical presence of the key limb patterning signalling centre, the apical ectodermal ridge (AER). Interestingly the opossum has a reduced AER in the forelimb compared to the mouse. In contrast, the tammar had a more pronounced AER in the forelimb than the hindlimb when compared to the mouse and opossum, although FGF8 expression was present in the ectodermal ridge of both the fore- and hindlimbs. Thus this thesis highlights the variability between marsupials in their limb development and the different mechanisms developed to achieve heterochrony. This study also provides the first assessment of homeobox genes, HOXA13 and HOXD13 in a syndactylous marsupial. These two key digit patterning genes showed high conservation of gene structure. However, there was slightly divergent expression of HOXA13 from that observed in the chicken and mouse. The expression of these HOX limb markers reflected the heterochrony between the tammar fore and hindlimb. The results in this thesis reaffirm the key role in digit patterning that HOX genes play. In addition the results highlights the evolutionary flexibility of retaining in the most common digit that is lost throughout evolution, digit one. Thus the loss of this digit potentially reflects the least evolutionary constraint. In contrast to the limb, the phallus undergoes an androgen-dependant virilisation stage. In most species this occurs in utero in which examination is not easy due to accessibility and also there can be interference from placental hormones. However, in the tammar, the young in accessible in the pouch and readily manipulated free from such disruption. Thus, this study is the first functional examination into the influence of androgens on phallic patterning gene expression in a marsupial. The results in this thesis suggest that SHH has a possible role in the proliferation and development of the marsupial phallus and that SHH could also have a role to prime the phallus for a later acceleration in development after the androgen-dependent phase. However, this study was restricted to the first 50 days post-partum. This raises the question of how androgen interacts with key patterning genes during later stages of development when the majority of phallus growth occurs. Considering the diversity in form between the limb and the phallus, it is essential to investigate alternative models. The macropodid marsupial which, like all marsupials, delivers a highly altricial young, but also has evolved a hopping mode of locomotion, shows both changes in timing of the development and differentiation of the limbs and phallus, making it an ideal model to answer questions about developmental processes. My findings using the tammar wallaby exemplifies the balance between selection and developmental constraints during evolution. The limb and phallus are unique examples in Nature which elegantly display the evolution of form and function. Taken together, this study exemplifies evolutionary flexibility in the development of appendages.
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ItemRole of oxygen in regulating embryo viability( 2013)Mammalian embryo development in vitro remains suboptimal compared to that in vivo, culminating in reduced viability and smaller foetuses. Cellular metabolism is fundamental to the successful development and function of any cell and perturbations in embryo metabolism have been linked to compromised viability post transfer. The preimplantation embryo displays plasticity and is adaptive in terms of nutrient utilisation. However metabolic adaption has a cost and, therefore, the potential to reduce embryo viability. By avoiding metabolic stress it may be possible to preserve the inherent viability of embryos during in vitro culture. Whilst media formulations have improved over the past 20 years, the culture environment in vitro remains static, which by its nature can lead to the introduction of artifacts. Physiological oxygen levels are around 5 to 7%, in contrast atmospheric oxygen (~20%) is commonly used in tissue and embryo culture. Consequently the overall objective of this thesis was to determine the role of oxygen in regulating embryo physiology and development. It is not known whether all stages of preimplantation embryo development are susceptible to oxygen toxicity. Therefore, the first study in this thesis investigated the temporal responses of preimplantation embryos to oxygen concentrations in vitro using time-lapse microscopy to continuously assess embryo development. Mouse preimplantation embryos were cultured in atmospheric (~20%) or lower (5%) oxygen concentrations for the first 48 hours, followed by culture in the same or reciprocal oxygen concentrations for another 48 hours: group 1 (control, 5 and 5%); group 2 (5 and 20%); group 3 (20 and 5%); and group 4 (20 and 20%). Compared with embryos cultured in 5% oxygen, embryos cultured in atmospheric oxygen were delayed at the 1st cleavage by 0.45 h (P<0.05), at the 2nd cleavage by 0.84 h (P<0.01) and at the 3rd cleavage by 3.19 h (P<0.001). Switching from atmospheric to 5% oxygen after 48 hours did not completely alleviate earlier induced perturbations. Partial or complete culture in atmospheric oxygen resulted in significantly fewer blastocyst cell numbers compared with control (P<0.05). These results identify that oxygen can influence mouse embryo development at both the pre- and post-compaction stages. A transient exposure to atmospheric oxygen can have a negative impact on embryo development, which is greatest prior to compaction and subsequent post-compaction culture at low oxygen cannot alleviate this damage. Oxygen is a powerful regulator of preimplantation embryo development, affecting gene expression, the proteome and consequently energy metabolism. Carbohydrate metabolism, which has linked to the ability of the mammalian embryo to develop in culture and remain viable after transfer, is affected by the relative oxygen concentration. The aim of the second study was, therefore, to determine the effect of oxygen concentration on the ability of mouse embryos to utilise both amino acids and carbohydrates, pre- and post-compaction. Metabolomic and fluorometric analysis of embryo culture media revealed that when embryos were exposed to atmospheric oxygen during the pre-compaction stages, they exhibited significantly greater amino acid utilisation and pyruvate uptake than when 5% oxygen was employed. In contrast, post-compaction embryos cultured in atmospheric oxygen showed significantly lower mean amino acid utilisation and glucose uptake. Furthermore, these metabolic changes are correlated with developmental compromise. Although ammonium has been shown to be embryo toxic, few studies have investigated the mechanism(s) by which the early embryo can regulate ammonium. Whilst atmospheric oxygen represents a source of stress to the developing embryo, it is not known how oxygen affects the physiology of the embryo in the presence of other sources of stress (combined stress). The aim of the third study was to investigate possible pathways involved in ammonium sequestration by the preimplantation embryo, and the effect of oxygen on the regulation of these pathways. Glutamine and alanine were investigated as possible ammonium sequestration pathways. Amino acid utilisation by blastocysts was determined after culture from the post-compaction stage with 0, 150 and 300 μM ammonium (in either 5% or 20% oxygen), and with or without 500 μM L-methionine sulfoximine (MSO), an inhibitor of glutamine synthetase. In the presence of MSO, ammonium production was significantly increased and glutamate was no longer consumed. Glutamine synthetase inhibition with MSO significantly decreased glutamine formation. Ammonium and oxygen independently altered overall amino acid turnover. Together, 5% oxygen and ammonium promoted glutamine production, whereas in the presence of atmospheric oxygen and ammonium, glutamine was consumed. These data reveal that both oxygen and ammonium affect the amino acid utilisation by the developing embryo, however atmospheric oxygen appears to have a greater detrimental effect. Consequently, mouse blastocysts can alleviate ammonium stress by its transamination to both glutamine and alanine, but only under physiological oxygen conditions. Leading edge technologies with increased sensitivity, such as time-lapse microscopy and LC-MS, were used to investigate the role of oxygen in regulating embryo viability. The use of time-lapse microscopy was essential in establishing the importance of physiological oxygen concentration during preimplantation embryo development. The studies described in this thesis demonstrated that an oxygen concentration beyond the in vivo range (5 – 7%) is a significant stressor to the preimplantation embryo leading to physiological variation, including developmental delays. Alterations in carbohydrate and amino acid utilisation suggest that the consequence of varying the oxygen conditions, to which the pronucleate oocyte experiences in vivo, is the activation of yet unknown pathways that alter the phenotype of these cells. The results within this thesis also identified the negative synergistic effects of atmospheric oxygen and ammonium, with the ability of the preimplantation embryo to regulate ammonium levels significantly compromised in the presence of atmospheric oxygen. These results have significant implications for interpretation of the literature particularly when atmospheric oxygen was employed during culture or diagnostic measurement, as the detrimental effects of atmospheric oxygen on the early embryo are irreversible and cumulative. Furthermore these data will facilitate the creation of better culture conditions and it is envisaged that this work will help improve IVF outcomes by reducing the number of attempts needed to achieve a live birth and improving birth outcomes.
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ItemSexual selection in cephalopods: multiple mating and sperm competition in dumpling squid (Euprymna tasmanica)( 2013)Sex differences in reproductive investment play a crucial role in sexual conflict. One intriguing aspect is conflict over mating frequency. In this regard, the evolution of female multiple mating (polyandry) has received particular attention, especially in systems where females receive no obvious direct benefits from males, and where mating is costly. Here, theory predicts that polyandrous females can increase their reproductive success by taking advantage of the genetic benefits of mating with multiple males. Cephalopods provide an interesting system for addressing this question because the great majority of species that have been studied mate multiply, with females storing sperm from multiple males, and sperm of many species have remarkable longevities. Mating is also likely to be costly in many species. Using the dumpling squid, Euprymna tasmanica, I examined differences in reproductive success between singly mated (monandrous), multiply mated (to the same male) and polyandrous (mated to two different males) females, controlling for recent male mating history and mating frequency. I found polyandrous females produced eggs faster and had larger hatchlings relative to egg mass than females mated once with a single male. These benefits are likely to outweigh the costs associated with mating and help to explain how multiple mating has evolved (or is maintained) in this group. In order to assess the natural level of multiple paternity and sperm use patterns in E. tasmanica, I developed five novel polymorphic microsatellites for this species, and measured the level of multiple paternity in clutches collected directly from the field, and from a series of clutches laid in the laboratory. All clutches measured had multiple paternity, with 2 – 4 sires per clutch, concordant with levels reported in other cephalopods. Clutches collected from the field had significantly higher levels of multiple paternity than those laid over an extended period in the laboratory, suggesting that females mate between laying bouts in the field. In order to understand sperm precedence patterns in this species I genotyped offspring produced from polyandrous females. Here I found that the last male to mate gains an advantage, siring up to 75 % of eggs at the beginning of the laying period. This level decreases to 54 % by the end of the laying period, suggesting that sperm are stratified within the female sperm storage organ at the beginning of the laying period and are more mixed by the end. Patterns of sperm precedence varied markedly among females and this variation was not correlated to any trait measured including male mass, copulation duration or the genetic relatedness of the mating pairs. The fact that all clutches had multiple sires might indicate that genetic diversity of offspring is an important driver of polyandry in this system. When examining mating behaviour in dumpling squid I found that male E. tasmanica perform more sperm displacement behaviour if the female has recently been mated, showing that they are able to determine the recent mating history of females. I found that sperm can be stored for a large proportion of their lifetime, up to 145 days. The data presented here represent a significant advancement in the knowledge of the evolution of polyandry and sperm use patterns in E. tasmanica and for cephalopods more generally.
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ItemABACuS: modelling the southern Benguela ecosystem with the Atlantis framework( 2013)This thesis describes the development, testing and implementation of ABACuS, an Atlantis model which was built to simulate the southern Benguela ecosystem and its associated fisheries. The southern Benguela is a highly productive marine ecosystem with intense upwelling, and supports fisheries with an average annual harvest on the order of 700,000 tonnes. Atlantis is a framework for building whole-of-system models to support fisheries management, and includes sub-models for the ecosystem and fisheries. Validation of the model was conducted using general pattern matching for biomass, spatial distribution and trophic interactions. System responsiveness was tested using a range of recommended ecosystem indicators such as mean length and age of fish in the system. The modelled system was perturbed using a range of fishing pressure scenarios, and the responses of the indicators varied in accordance with the expected behaviour of indicators in the real system, suggesting that the model is useful for testing alternative fishing strategies. The inherent complexity of ecosystem models makes comprehensive assumption analysis extremely challenging. To explore the implications of the governing assumptions of different models, the behaviour of ABACuS was compared with two other ecosystem models of the southern Benguela, built in OSMOSE and Ecopath with Ecosim. The three models differed in their representation of spatial resolution, population structure and trophic interaction mechanisms between model groups. Two fishing pressure scenarios were applied to all the models, increasing fishing on either small pelagic planktivores (sardine, round herring and anchovy), or large demersal piscivores (two species of hake). The model outputs were analysed using a suite of ecosystem indicators, and the overall system behaviour was similar in all models despite major differences in model formulation. Indicators that aggregated modelled species by trophic level had generally poor agreement between models, so an alternative aggregation method was explored. Grouping model species by functional guild in each model provided system responses that were more robust to model choice, and are suggested as an area for further study. Fisheries management is typically informed by single-species stock assessment models that omit explicit representation of the broader system. The ecosystem effects of interactions between multiple fisheries were explored in the model. The total summed harvest that was achieved by fishing multiple modelled species at their individual F(MSY) was compared with the total harvest achieved by fishing all the modelled species simultaneously at their F(MSY) level. Contrary to intuitive expectation (and previous modelling work focusing on more demersal marine fish communities), the simultaneous harvest was greater than the sum of individual harvests. These results were further explored using qualitative models and by studying the influences of trophic interaction between species at different levels of the foodweb, and the overall result was found to be driven by two key factors: volumetric dominance of small pelagic fish in the total catch, and asymmetric influences of competition and predation between piscivorous and planktivorous species. This work has important implications for the design of tactical multi-species models for use in ecosystem-based fisheries management.
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ItemThe importance of environmental flows to the spawning and larval ecology of black bream (Sparidae: Acanthopagrus butcheri)( 2013)In this thesis I investigate the link between environmental flows and black bream, (Acanthopagrus butcheri) productivity in the Gippsland Lakes in south-eastern Australia. Environmental flows describe the quantity, timing and quality of freshwater flows to maintain a healthy ecosystem. This is of particular importance to estuaries which are highly productive ecosystems supporting many fisheries. Over the past decade, there has been increasing evidence of a link between environmental flows and catch per unit effort (CPUE) data. Many studies have attempted to understand the basis of this relationship but with limited success. The focus of this thesis is on black bream; an iconic species that supports large recreational and commercial fisheries. Black bream is also unique in that it completes its entire life-cycle within a single estuary. In recent decades there has been a marked decline in commercial catches of black bream that has coincided with a decline in freshwater flows. Although such declines are often blamed on fishing pressure, it is possible that environmental flows underpin this pattern. In 2007, I sampled 23 sites, including the lakes and three tributary rivers, to establish the temporal and spatial distribution of black bream eggs and larvae. Using oblique plankton tows, I established that black bream spawned from September through to December with egg concentrations peaking in October. Black bream eggs were found in similar concentrations throughout the lakes and rivers. However, more than 99 % of larvae were collected from within rivers, with very few larvae being collected from the lakes. A comparison of two spawning seasons revealed that the year with higher freshwater flows also had greater spawning activity and higher concentrations of larvae. Interestingly, there was a significant relationship between the distribution of eggs and larvae with the level of stratification. The highest concentrations of larvae occurred at sites with a difference in bottom and surface salinities of 15-20. In 2008, I altered the sampling methodology to use stratified plankton tows to establish both vertical and horizontal distribution of eggs, larvae and prey. I collected eggs, larvae, zooplankton and water quality data at multiple depths from eight sampling sites over seven fieldtrips from August to December 2008. Spatial coupling between black bream larvae and copepods and the halocline was observed in the upper estuary. Nauplii of the copepod Gladioferens pectinatus, an important prey species for larval fish, dominated the zooplankton assemblage (>80 %) and larval gut contents. This part of the thesis demonstrates that freshwater flows and the generation of salinity stratification have a large influence on the size of suitable habitat for larval bream. Adult black bream are more prevalent in salinities in the range 15-25 and I hypothesised that environmental flows would therefore also influence the location of mature fish. With the use of acoustic transmitters and receivers, I was able to tag fish and monitor their locations for up to ~450 days. I implanted VEMCO V9 acoustic transmitter tags into 41 black bream between July and August 2008. Over the same period, 25 estuary perch, an iconic estuarine fish species that is believed to having contrasting ecology to black bream, were also tagged. Receivers were placed at 2 km intervals from the river mouth in both the Mitchell and Tambo Rivers. Black bream were highly mobile, with distinct temporal patterns, including tagged fish moving to the upper estuary in late winter and remaining until early summer before returning to the lower estuary. In contrast, estuary perch were highly site attached and only moved short distances with the exception of a distinct downstream migration during significant freshwater flow events. Generalised linear models revealed a significant effect of freshwater flows on the positions of tagged fish, with a greater effect in the Mitchell River compared to the Tambo River. Moon phase also had a significant effect, with tagged fish moving further upstream during a full moon compared to the new moon. The effect of moon phase was much greater for black bream. Unlike juvenile and adult fish, tagging techniques are not suitable for studying larval fish movement, dispersal and connectivity. I therefore aimed to investigate if the otolith microchemistry of larval black bream could be used to determine natal origins and dispersal patterns throughout an estuary. The otolith or ear bone of a fish is often referred to as a ‘black box recorder’; growing continuously whilst incorporating chemical elements into the calcium carbonate structure. These elements and their corresponding concentrations are often reflective of the water chemistry the fish are residing in. I collected larvae and water samples from sites in the Mitchell and Tambo rivers. I analysed both larval otoliths and water for a suite of elements to determine whether they could be used to distinguish between intra- and inter-estuary variability. Water samples from both the Mitchell and Tambo rivers revealed three significant water layers (freshwater, halocline and marine waters) based on their chemical signature. Sufficient otoliths from larvae for analysis were collected from the Mitchell River. Significant spatial and temporal variability in otolith chemistry was detected, however, the level of variability was limited to broad spatial scales of upper and lower estuary and halocline and marine layers. Further research is needed to validate this potential use of otoliths. The findings of this thesis have highlighted the importance of sufficient environmental flows to establish and maintain optimal conditions for black bream spawning and larvae. While this study concentrate on one species, these results can be applied to other species of estuarine resident and dependant fishes. As estuaries are highly susceptible to the impacts of climate change and anthropogenic estuaries, so are the fluctuations of year-class strengths of fishes that rely on estuaries. These finding have and will assist managers of catchments, environmental flows and fisheries to ensure that our aquatic environment and fisheries are managed sustainably into the future.
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ItemUsing Chironomidae to assess water and sediment quality( 2013)Biological assessments with Chironomidae (chironomids) are often used to provide information on the causes and effects of aquatic pollution. However, these applications are constrained by several factors, some of which were investigated in this thesis. Laboratory toxicity test results are used to determine toxicity in the field, but these are ecologically irrelevant and often fail to account for the influence of complicating factors in the field. Two such factors are food limitation, potentially caused by an indirect effect of pollution, and the exposure of previous generations to stressors. The effect of food limitation was investigated in a multigenerational laboratory experiment with Chironomus tepperi. Responses to food limitation were similar to toxicity, with reduced survival, reproduction and increased development times as food became limited. The offspring of food limited parents were also affected. There was evidence that the quality of these offspring were compromised, even when offspring were raised under standard food conditions. Males and females responded differently, with greater developmental delays seen in female offspring. There is also a scarcity of data regarding the effects of various pollutants on different chironomid species, particularly for Australian chironomids, under ecologically relevant conditions. In field-based microcosm experiments the effects of 17α-ethinylestradiol (EE2), tebufenozide and diuron were investigated. High nominal concentrations (10 μg L-1) of EE2 consistently induced a novel antennal deformity in Procladius species larvae, but no effects on assemblages, abundances or development rate were observed except for an increased number of taxa at lower concentrations. Similarly, aside from increasing the number of taxa at the lowest nominal concentration of 0.004 mg L-1, diuron had no effect on assemblages or species. Tebufenozide had no effect on these parameters. Another constraint is an inadequate understanding and insufficient use of alternative endpoints, such as sex ratio skewing and adult responses in situ. Experimental studies showed that sex ratio skewing was stressor specific, occurring after exposure to tebufenozide and diuron but not EE2 or food limitation. It was also species specific; tebufenozide and diuron caused skewing in different species. There was evidence that skewing was consistent, with the feminised sex ratios in Procladius villosimanus caused by diuron similar to that in P. paludicola in a previous study. In addition to sex ratios, other adult endpoints such as abundance and diversity are also useful for measuring impairment, although these are rarely including in biomonitoring studies. To measure adult responses in situ a method was developed using yellow sticky traps. The method was successfully able to detect differences between sites based on the composition and sex ratios of the chironomid fauna captured. Some of these biological parameters could be related to zinc pollution in sediments. The results of these studies demonstrate the value of considering factors aside from toxicity, continued pollutant testing and the use of alternative endpoints in bioassessments with chironomids. Multigenerational testing and measuring sex ratios should be routinely included in studies with chironomids and, along with adult biomonitoring, represent useful additions to current approaches that need further investigation.
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ItemFactors and processes affecting co-management of natural resources( 2013)Managing renewable natural resources is difficult because of the complexity of their interlinked social and ecological components. In this context, co-management, where management responsibility is shared between government and resource-users, may improve the suitability and perceived legitimacy of management rules. However, despite the potential for such arrangements to improve the resilience of natural resource systems, how co-management works remains poorly understood. By comparing five abalone fisheries from south-eastern Australia, I develop a more thorough understanding of the factors and processes that influence the success of co-management arrangements. Each of the five abalone fisheries studied here has, to varying degrees, adopted management rules above those required by government. This includes higher size limits, area-specific catch limits, closed areas and requests for quota cuts. I use semi-structured interviews, questionnaires and observations of collaborative management workshops to explore these initiatives and the factors that have helped or hindered their implementation. Higher levels of trust and cooperative capacity enabled greater levels of industry-based resource management in four of the five fisheries. In one case, however, high levels of trust did not translate into concomitant levels of resource management. This case is evidence that additional factors, such as perceptions of resource condition, are key determinants of resource stewardship. Expanding out from this central relationship, there appears to be a broad range of factors and processes that interact to affect stewardship behaviour. In the fisheries studied here this included factors such as leadership, group size, the support of government and perceptions of the fairness of industry management forums. Interestingly, at the level of individual stakeholders, private rights do not appear to be as important in influencing stewardship behaviour as is often assumed. In the current study, the management preferences of quota owners were no more conservative than those of contract divers, who do not own any resource rights. These results indicate that private property rights, such as individual transferable quota, may be less important in generating stewardship behaviour than as suggested by other studies. Finally, this thesis describes how the process of collaboration and adaptive co-management can, in itself, help to build the trust and knowledge necessary for effective management. For this to occur, resource users, managers and scientists need management forums that are open, deliberative and that repeat over time. This provides for social learning, iterative decision-making and, ultimately, a capacity and flexibility for adapting to change.
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ItemPredicting responses to climate change: ecophysiology of the common brown butterfly, Heternoympha merope( 2013)Understanding the processes through which climate limits the distribution and abundance of organisms is a fundamental question in ecology, and is particularly important in light of recent, on-going, climate change. Variation in temperature in particular, can have substantial impacts on the fitness and survival of organisms, through its ubiquitous effects on biological rates. However, animals have the capacity to construct their own thermal environment through behaviour, and so to understand the impacts of temperature on species’ ecology, interactions between the organism and its environment must be accounted for. Holometabolous insects make fascinating systems with which to explore the impacts of temperature on fitness, because the different life-cycle stages vary in thermal sensitivity, their capacity to behave, and in the environments encountered. Furthermore, the different life-history stages are invariably linked: conditions experienced by one life-cycle stage have a direct impact on the fitness and survival of subsequent stages and generations. Consequently, understanding how climate constrains the survival of such species requires a holistic approach, in which all stages of the life-cycle are considered. This thesis focuses on an endemic, widespread Australian butterfly, the common brown, Heteronympha merope. To ascertain how the life-cycle phases of H. merope differ in their thermal sensitivities, I measured the impact of temperature on a suite of fitness traits including development time, growth rate, body size, flight, longevity, starvation and fecundity. As adult butterflies have a broad scope for behavioural thermoregulation, I also quantified how basking posture affects the core-body temperature of H. merope. These empirical datasets were subsequently incorporated into a mechanistic model, which was run across the Australian landscape with high-resolution, spatial climatic datasets to identify processes that constrain H. merope’s distribution. These models incorporate variation in thermal sensitivities, behaviour and dispersal potential of the different life-history phases to attain a comprehensive understanding of how climate limits the common brown’s survival. The final model provides a powerful tool for holistically assessing how organisms with complex life cycles, such as butterflies, are likely to respond to future climate change.