School of BioSciences - Theses
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ItemBirds in the sky, fish in the sea, money in the bank: quantitative methods for more effective conservation( 2021)My approach in this thesis was to explore how to wring more information out of existing data to reduce uncertainty, improve decision-making and hope to generate better conservation outcomes. I explore and develop a range of quantitative tools to this end. I look at three key areas: dealing with uncertainty, structuring decision making, and improving the use of existing information. I consider these concepts over three thematic case studies: monitoring the abundance of three vulture species in Cambodia, trading-off the costs and benefits of releasing information publicly when a new species or population is discovered, and comparing use of optimisation and project prioritisation protocols to allocate funding to species conservation efforts. In the first case-study, I develop new Bayesian hierarchical model to estimate vulture abundance, and compare the inferences available from this approach with less specialised approaches previously used. In the second case-study I develop a decision-making framework to allow decision-makers to explicitly trade-off costs and benefits, and apply the method to data collected from informants who have made these types of decisions themselves. In the final section, I explore whether additional information can improve optimisation to allocate funding, and compare performance in terms of expected avoided extinctions of the optimisation approach with a project prioritisation protocol. I find that there is indeed much more we can learn from the information we have. But this is not a free lunch – work needs to be done to uncover opportunities, and technical skills are often needed to make best use of them, and assumptions must often be made to draw conclusions.
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ItemTesting the decline of the threatened New Holland Mouse (Pseudomys novaehollandiae)( 2019)Delineating the distribution of a threatened species is critical for identifying threats and guiding conservation management. The process is challenging, however, especially when a species is rapidly declining, and so changing its distribution. In this context, species distribution modelling (SDM) often lacks the precision needed to inform fine-scale management decisions, but on-ground surveys to test species’ distributions are time and resource intensive. The dilemma can be mitigated to some extent by careful examination of historical data, and optimal monitoring. The New Holland Mouse (NHM; Pseudomys novaehollandiae) is one of many Australian rodent species to have undergone drastic distributional declines since European invasion. Initially recorded in Victoria in 1970, by 2015 NHMs were thought to occur in only 3 of 12 historically occupied regions. I tested this decline with statistical rigour, using extensive Elliott and camera trapping surveys at >500 sites across Victoria. Combining my survey data with 48 years of others’ efforts, I evaluated the utility of standard Elliott trapping surveys and the efficacy of camera trapping for NHMs. I tested whether NHMs were where we would expect based on state-government threatened fauna SDMs, and whether the species’ purported early-successional fire association explained occurrence or abundance. I confirmed the species’ persistence in 5 of 12 historical regions – including regions where NHMs had not been detected in 5-21 years – and expanded the species’ known distribution in two regions. However, these finds can be attributed to a paucity of prior survey effort and were partnered with greater declines elsewhere. Elliott trapping surveys were often inadequate to provide statistical confidence in the species’ absence; camera trap surveys provide a viable alternative for distribution assessments. Standard state-government SDMs provided limited guidance as to the true distribution of NHMs and SDMs for declining species should be interpreted with caution. Time-since-fire did not explain the species’ occurrence and poorly explains abundance, though in certain locations inappropriate fire regimes are a threatening process. Predator control, habitat management, and careful reintroductions are key priorities for conservation of NHMs in Victoria.
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ItemContrasting population responses of ecologically-similar sympatric species to multiple threatening processes( 2015)Understanding drivers of population change is crucial when species are declining. However, uncertainty about species declines and causal factors are pervasive problems hampering conservation efforts. This is because populations can naturally fluctuate and pre-decline population data are often insufficient to diagnose causes of decline which may be driven by multiple threats, environmental processes and possible interactions. Globally, amphibians are declining at a rate exceeding other assessed vertebrate taxa. Chytrid fungus (Batrachochytrium dendrobatidis) is a key threat that has caused rapid amphibian declines. However, species and population responses to chytrid can vary and may be influenced by interactions with sympatric species, climatic conditions or other threats. Understanding why species respond differently to chytrid is crucial as few options currently exist to manage the threat. I examined a case for the critically endangered Spotted Tree Frog (Litoria spenceri) and the non-threatened Lesueur’s Frog (Litoria lesueurii). Litoria spenceri has been recorded at 50 sites at elevations of 300 - 1110m asl in south-eastern Australia. Litoria lesueurii co-occurs at some sites but has a much broader distribution. Both are stream-breeding species that respond differently to introduced trout (Salmo trutta and Oncorhynchus mykiss) and were suspected to respond differently to chytrid. I constructed a two-species dynamic occupancy model to examine the historic and future changes in site occupancy of both frog species, and evaluated factors that influence their probabilities of local extinction and colonization. Models combined fragmented historic data and more intensive post-decline data collected over a 55-year period (1958-2012) at 49 historic L. spenceri sites. Trout influence could not be examined as they occurred at all but one site. My analysis revealed that L. spenceri has declined from approximately 50% of known historic sites. This decline could be influenced by either (or both) the presence of chytrid or the presence of L. lesueurii, but was most severe when both chytrid and L. lesueurii were present at sites. In contrast, L. lesueurii tended to become more prevalent over time and changes were uncorrelated with the occurrence of chytrid or L. spenceri. Without intervention, the model extrapolated that L. spenceri will continue to decline, and may be extinct by as early as 2035. I hypothesize that L. spenceri decline is most severe at sites when the presence of pathogen-host-reservoir species (or total frog density) facilitates chytrid persistence and maintains chytrid transmission. Several PCR tests exist to detect chytrid but their results may be imperfect. Prior to evaluating the impact of chytrid on wild frog populations, I assessed the diagnostic sensitivity and specificity of a Qiagen quantitative PCR method to detect chytrid using spiked samples. The Qiagen quantitative PCR was selected as preliminary results indicated equal or superior sensitivity to other published methods. The Qiagen diagnostic sensitivity was high (mean generally > 0.937) but varied in response to the concentration of zoospores in the sample. Diagnostic sensitivity could be improved by classifying equivocal results as positive, with minimal impact on diagnostic specificity. Mean diagnostic specificity was 0.961 (95% CI: 0.897-0.995). The results highlight a risk of misclassifying samples due to imperfect diagnostic sensitivity and specificity which should be considered by practitioners when evaluating the impact of disease on wildlife. To clarify the response of L. spenceri and L. Lesueurii to chytrid I assessed the infection state of all frogs each time they were encountered during a four – six year mark-recapture study at 4 sites. I quantified individual’s probabilities of infection, recovery from infection and survival in each infection state using multi-infection-state models. Nine candidate models were compared to account for four factors that could bias parameter estimates: 1) potential misclassification of disease state, 2) disease state affecting detection, 3) impacts of marking on survival or capture probabilities, and 4) the assumed ability of individuals to recover from an infection. The model with the most support (lowest DIC value) for both species assumed some misclassification of an individual’s disease state, equal detection of infected and uninfected frogs, no effect of marking on return rates, and that frogs could recover from an infection. Marking did not reduce the probability of capture or survival of L. lesueurii and the impact upon L. spenceri was uncertain. Chytrid infection reduced the survival of both species. Litoria lesueurii had the higher probability of becoming infected and the lower probability of survival when infected. Both species had similar probabilities of recovery from infection. Discrete-time deterministic multi-state population models were constructed using multi-state mark-recapture and published parameter estimates to assess the combined influence of chytrid and introduced trout upon each frog species. High, mid and low elevation site models were constructed for each species to reflect demographic differences that are known to be correlated with climate and elevation. Age to maturation, clutch size and egg-year1 survival influenced interspecific and intraspecific population-level responses of the two frogs to threats. Crucially, L. spenceri populations were non-viable at high and mid elevations but had some capacity to persist at low elevations when impacted by both threats (in the absence of stochastic processes and pathogen reservoir species). In contrast, L. lesueurii populations had a greater capacity to persist at both low and mid elevation sites. This thesis highlights that population dynamics and the causes of decline must be carefully evaluated to understand species’ contrasting responses to multiple threats and to identify effective conservation management solutions. Chytrid can severely impact both threatened and non-threatened frogs at an individual-level. However, species population-level responses to chytrid are influenced by their ability to compensate for pathogen-induced mortality through recruitment. Interspecific and intraspecific differences in amphibian populations’ risk of extinction can occur when species recruitment is influenced by site-specific environmental processes and other threats. Furthermore site-specific extinction risk may also be exacerbated by the presence of native sympatric species that act as pathogen reservoir hosts or competitors. In this case, mitigation of threats to L. spenceri might be achieved at some sites by enhancing recruitment through trout management. However, trout mitigation may increase chytrid infection risk, which should be monitored and potentially concurrently managed. Prudent management action is required for species like L. spenceri that are facing multiple threats to avoid undesirable conservation outcomes and to prevent extinction.
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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.