School of BioSciences - Theses
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ItemTargeted gene flow for conservation: northern quolls and the invasive cane toad( 2018)Global biodiversity is declining at an unprecedented rate. Within declining populations, however, there are some individuals who are able to survive the threat. Unfortunately in many cases these adaptive traits are not common enough to prevent extinction, particularly when threats are rapid and severe. But by understanding how species respond to certain threats conservationists may be able to boost adaptive potential in threatened populations. Targeted gene flow is a novel conservation tool that involves moving individuals with relevant traits to areas where they could be beneficial for conservation. Although the implications are wide reaching, this idea is yet to be attempted on a wild population. In this thesis, I set out to test the feasibility of targeted gene flow as a conservation tool, using the endangered northern quoll (Dasyurus hallucatus) as a model species. Northern quolls have experienced dramatic declines since the introduction of the invasive cane toad (Rhinella marina) because the quolls unsuspectingly attack the toxic toads. There are, however, a small number of remnant quoll populations that have survived the toad invasion, seemingly because they do not attack toads. It is this potential “toad-smart” behaviour I hoped to harness using targeted gene flow. If it was possible to breed toad-smarts into still threatened areas of the northern quoll’s range, managers could boost adaptive potential and population survival. The first step was to understand how some individuals could survive alongside toads. In the preliminary chapters of this thesis, I examine toad-exposed northern quolls to see how they react to cane toads. I found that quolls from areas invaded by cane toads were indeed toad-smart – they didn’t attack toads. Using a common garden experiment, I then demonstrated this toad-smart behaviour had a heritable basis, meaning I could potentially breed the trait into threatened populations. The next step was to explore how best to implement targeted gene flow for quolls, including investigating any potential negative impacts. I used population modelling to explore the optimal timing and number of individuals introduced to maximise population survival whilst maintaining species-level genetic diversity. I then set up an experimental field trail, releasing both toad-smart and toad-naïve northern quolls onto a toad-infested island. Despite unforeseen circumstances that resulted in a dramatic reduction in population size, I was able to demonstrate no negative implications of targeted gene flow from the first stage of the experiment. This thesis shares the process of exploring a new conservation strategy, from initial conception to field trials. I provide evidence that targeted gene flow could reverse declines of threatened northern quoll populations – demonstrating a genetic basis for toad-smart behaviour, showing little evidence of outbreeding depression, and presenting the ideal management approach for implementing the tool in threatened populations. The resulting strategy is not limited to northern quolls, but instead has widespread applications for other threatened populations. Even the most endangered populations often have some individuals who are resistant to a threat. If conservations can understand and harness these adaptive traits, targeted gene flow could prove an invaluable tool for conserving threatened species.
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ItemHabitat preferences and fitness consequences for fauna associated with novel marine environments( 2017)The rapidly expanding reach of anthropogenic environmental change means that animals must now navigate landscapes comprised largely of modified and degraded habitats. Individuals that correctly perceive habitat quality will be best placed to survive and reproduce in novel environments, but where environmental change outpaces the evolution of behavioural responses, mismatches can arise between cues and the underlying value of habitats. These mismatches can lead individuals to select habitats that offer relatively poor fitness outcomes, creating ecological traps. In environments where ecological traps are likely to occur, data on habitat preferences and fitness consequences can fundamentally change predictions of metapopulation models and increase our understanding of the role that novel habitats play in population persistence, but such data are rarely collected. In this thesis, I first conduct a global meta-analysis to assess the state of knowledge on habitat preference and fitness metrics in animal populations, using wildlife populations associated with aquaculture as a case study. My findings reveal that responses to aquaculture vary widely across taxa and farming systems, ranging from large increases in abundance to near complete displacement. However, the influence of aquaculture on wildlife populations remains poorly understood, as researchers rarely obtain appropriate measures of habitat preference, survival or reproductive success. Accordingly, in subsequent chapters I apply the ecological trap framework to assess marine habitats modified by aquaculture or invasive species. In the first application, I collect wild Atlantic cod (a species known to be attracted to salmon farms) from areas of high and low salmon farming intensity, and compare reproductive fitness via a captive spawning trial with hatchery-rearing of offspring. I found limited negative effects of high farming intensity on quality of offspring. In the second application, I show that the threat of predation by a native keystone predator may limit the ability of an invasive seastar to exploit a food-rich habitat at shellfish farms. In the third application, I show that an invasive canopy-forming marine macroalga provides viable habitat for native fishes and may help to maintain fish biodiversity in areas where urban impacts have driven a decline in native macroalgal canopy cover. Together, this thesis demonstrates the utility of individual-level data on habitat preference and fitness outcomes—via the application of the ecological trap conceptual framework—in assessing the impacts of novel habitats on animals, and recommends greater use of this approach in future investigations into the impacts of human-induced rapid environmental change in coastal marine ecosystems.
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ItemTraits-based and perception approaches for management of invasive exotic species from tropical botanic gardens( 2018)The factors driving plant invasion are key questions in invasion ecology. Traits also can act as indicators of plant invasion processes. If traits are proven to be a significant proxy for plant invasiveness, then invasiveness of exotic species may be efficiently predicted by measuring traits. Botanic gardens have consistently supported ex-situ plant conservation, research, and environmental education. However, botanic gardens can also be pathways of exotic invasive species introduction. Botanic gardens should become a strategic stakeholder for exotic invasive plant species management. For exotic invasive species management, we cannot solely rely on ecological approaches. Social perception is an important component of invasive species management. Social perception may become either a problem or a solution for invasive species management. These perceptions should be clarified among relevant stakeholders to minimize conflicts of interest among relevant stakeholders of invasive species management. This study focuses on invasive plant species in tropical environments and the aim of this study is to answer the following questions: (1) Focusing on the relationship between exotic species abundance and traits in the tropical ecosystem, what traits or sets of traits are relevant and useful as proxies for examining the relationship between traits and local abundance in invaded tropical forest ecosystems? Assuming biological characteristic of invaders involved in the invasion pathways, what are the plausible and relevant traits?; (2) To what extent can these selected traits explain the proxies of invasion processes: local abundance and dispersal distance of naturalised exotic collections of botanic gardens in native ecosystems?; (3) To what extent these selected traits may be useful to differentiate naturalised from non-naturalised exotic collections?; (4) How robustly can the traits explain the detectability of exotic plant species in tropical rainforests adjacent to botanic gardens?; and (5) What are the perceptions of internal stakeholder’s (staff of botanic gardens) of exotic and invasive plant species? Assuming they like these exotic species, what are the reasons? I conducted literature review studies from relevant resources to answer question 1. Then, I conducted trait-based studies to answer questions 2, 3, and 4 by examining local density, their spread distance from gardens, and measured relevant traits of these detected naturalised exotics. The study sites consist of four Indonesian botanic gardens (Bali, Baturraden, Cibodas, and Kuningan) and their adjacent native forest ecosystems. I used Biophilia theory to examine the positive perception of botanic gardens staff on exotic invasive species to answer question 5. By analyzing data that was collected during line transect distance sampling surveys, I used a multi-species hierarchical distance sampling model to evaluate how plant height, leaf size, leaf shape, and survey location influence exotic species detectability. Detectability of these exotics increased with plant height and leaf size. This study demonstrates the effect of plant height and leaf characteristics on the detectability of exotic species. The results of this study also indicated that information on traits might improve predictions about exotic species detection, which can then be used to optimize the allocation of the search effort for efficient species management. I showed that SLA strongly differentiates naturalised from non-naturalised botanic gardens’ exotic collections. This finding suggested that exotic species plausibly relied on high growth rate and forest opening gaps to establish in the tropical forests. I showed that traits can strongly differentiate naturalised from non-naturalised exotic species and this is a good sign for trait-based risk assessment application in the tropics. In general, the dominionistic type dominated the social perception of botanic gardens’ staff towards exotic invasive plant species. There was only minor variation in perception type dominance across demographic factors. These findings indicate that the inspiration to manage or ‘to rule’, and curiosity to learn about exotic species were the main motivations behind the Biophilia-based perceptions among Indonesian botanic gardens’ staff. This information may help to enhance strategies to increase stakeholders’ involvement in exotic invasive species management and to avoid or minimize conflict of interests among stakeholders. I demonstrated that traits are a useful proxy for multiple aspects of exotic invasive plant species management, particularly for botanic gardens. I also showed that social perceptions can be quantified effectively and Biophilia theory is a relevant framework to analyze the social perception of exotic invasive plant species. We cannot simply rely on ecological traits to support exotic species management. Exotic species can benefit humans, so human perception and behavior are also a critical consideration for exotic species studies either in botanic gardens or in general. For invasive species management contexts, social aspects should be synergized with ecological aspects to maximize social acceptance and minimize conflict of interest among stakeholders. This, in turn, will link the exotic invasive species management plan and its implementation in practice.
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ItemOptimal resource allocation for invasive species management( 2016)Invasive species are responsible for enormous ecological and economic damage worldwide, and resources for managing them are severely limited. Allocating these resources efficiently is therefore a key concern for conservation managers. Unfortunately, the complexity of the problem makes developing cost-effective strategies for managing invasive species extraordinarily difficult. The scale and difficulty of the problem highlights that quantitative approaches are needed to both understand the general properties of a good control strategy and to assist in developing invasive species management plans in specific cases. In this thesis I use mathematical modelling to find optimal strategies for invasive species control. The theoretical work contained here focuses on solving for the optimal resource allocation in spatial, temporal and spatiotemporal systems. This gives insight into the qualitative features of optimal management. Moving from purely spatial or temporal optimal solutions to the full spatiotemporal solution increases the complexity of the models and solutions. However, key ideas about invasive species control in the spatial and temporal sections translate to the spatiotemporal problem, and a good understanding of these results in this thesis allow one to better understand solutions in the more complex spatiotemporal case. As well as general insights, I want to offer specific support to environmental managers; mathematical modelling is applied to three case studies in this thesis. The first two are applications of optimal control theory to feral cat (Felis catus) control in arid Australia and to orange hawkweed control (Hieracium aurantiacum). The third case is about the proposed eradication of tropical fire ants (Solenopsis geminate) from the islands of Ashmore Reef Commonwealth Marine Reserve in the Timor Sea, which is off the Northwest coast of Australia. This work focuses on providing quantitative advice about the management of tropical fire ants. Linked models for the population dynamics and detectability of tropical fire ants are developed. These models quantify how different control methods and schedules affect the probability of eradicating ants and allow the resource allocation for surveillance to be optimised.
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ItemOptimal management of metapopulations across space and time( 2016)Many threatened and invasive species occupy collections of spatially separated populations subject to local extinction and colonisation, known as metapopulations. Although they occur naturally, metapopulations are becoming increasingly prevalent throughout the world due to habitat loss and fragmentation. To increase the persistence of threatened metapopulations, or decrease the persistence of invasive ones, managers must decide how, where and when to spend limited resources across space and time. In this thesis, I integrate quantitative models with decision theory to predict the persistence of metapopulations in response to management alternatives. This thesis is divided into six chapters. The first chapter provides a general introduction to metapopulations and decision theory. The second chapter explores when, where and how to manage threatened metapopulations when the dynamics of these networks are poorly understood. Adaptive management has been applied to ecological problems containing considerable uncertainty, but is yet to guide the restoration of metapopulations. I develop a framework to optimally manage metapopulations using adaptive management when there is uncertainty in the rate of colonisation between patches. I develop a case study for the threatened bay checkerspot butterfly (Euphydryas editha bayensis) and demonstrate how best to manage the population while learning about its dynamics over time. The third chapter examines when to add a patch to a threatened metapopulation to compensate for destruction of another due to urbanisation or agricultural development. I develop spatially explicit metapopulation models for two threatened Australian species – the growling grass frog (Litoria raniformis) and the southern emu-wren (Spititurus malachurus intermedius) – and determine when it is optimal to add a patch to each metapopulation if the budget available to managers accrues interest over time. I find that there are many occupancy states of each metapopulation where it is optimal to delay habitat creation until well-after habitat destruction has occurred. The second half of this thesis focuses on invasive metapopulations. Chapter 4 develops a rule for determining when to increase the colonisation rate of metapopulations susceptible to three types of threat – an abiotic threat (i.e. fire, flood or drought), a generalist threat, and a specialist threat (i.e. predators, pathogens or disease). When considering habitat corridors as a management strategy, I show that managers must consider not only the type of threat acting on a metapopulation, but also how a threat might also respond to increased colonisation of a focal species. In some instances, increasing the colonisation rate can be detrimental to metapopulation persistence because of increased exposure to threats occupying the same habitat. The fifth chapter examines which patches of suitable habitat should be managed to contain the spread of one of the worst invasive species in Australia, the cane toad (Rhinella marina). A previously published model predicts the spread of toads can be contained by managing as few as 100 artificial water bodies (such as dams) in north-west Australia. I revise this model to address concerns raised by potential end-users, and find the most cost-effective location for a barrier to contain toad spread. In all of the scenarios tested cane toads could be contained from moving west from Northern Australia, at a cost of approximately $4.5 million over the next 50 years. Finally, Chapter 6 summarises the main findings of this thesis and discusses important areas of future research.