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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ItemImpacts of streetlights on sleep in urban birds( 2019)Over the past century, artificial light has dramatically transformed our environment. Light at night is increasing globally, to the extent that in many places, true darkness no longer exists. As the timing of light can influence almost all aspects of biology, the alteration of natural light cycles could pose a severe threat to wildlife. One particularly harmful impact could be the disruption of sleep. In this dissertation, I investigate the impacts of artificial light at night on sleep. Despite the importance and prevalence of sleep across the animal kingdom, sleep is arguably underappreciated in studies of ecology and conservation. After providing a general introduction (Chapter 1), I begin by giving a broad perspective of sleep research, including current methods, opportunities, and the significance of sleep for issues such as artificial light at night (Chapter 2). I then provide a review of the evidence for impacts of artificial light at night, in both humans and wildlife (Chapter 3). Finally, I explore the effects of artificial light at night on two diurnal bird species: pigeons (Columba livia) and black swans (Cygnus atratus). I focus on the effects of one of the most common sources of outdoor lighting: streetlights. Light at night from LED streetlights caused pigeons to have less rapid eye movement (REM) sleep and non-REM sleep, have more fragmented sleep, and sleep less intensely than during darkness (Chapter 4). Some of these effects persisted for more than a day after exposure to light at night. In black swans, light at night in a naturalistic environment reduced night-time rest, which we demonstrate reflects reduced sleep (Chapter 5). This research provides the first direct evidence that exposure to environmentally-realistic artificial light at night can disrupt sleep in birds. One possible strategy for reducing disruption of sleep could be to alter the colour of lighting. To test this idea, I compare the effects of two different lighting colours: white (blue-rich) and amber (blue-reduced) light. Previous research has shown that blue wavelengths of light have the greatest effect on melatonin, a hormone important for sleep regulation. However, contrary to my predictions, amber and white light had very similar effects on sleep in both pigeons (Chapter 4) and swans (Chapter 5). Together, these findings will help councils and other land managers to make more informed decisions about lighting, particularly for areas that might offer important refuges for wildlife.
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ItemTaxonomy, ecology and conservation genomics of North-Eastern Australian Earless Dragons (Agamidae: Tympanocryptis spp.)( 2018)Land clearing and modification of natural habitats is threatening biodiversity globally. In Australia, most native grassland habitats have been heavily modified for agriculture, including cropping and grazing. Grassland specialist species, including earless dragon lizards (Tympanocryptis spp.) in north-eastern Australia, are of conservation concern due to this continued habitat loss and fragmentation. However, the north-eastern Australian group of earless dragons (including the recently described T. condaminensis, T. wilsoni and T. pentalineata) are at significant risk, due to the presence of multiple undescribed cryptic Tympanocryptis lineages within this region. It is imperative that the taxonomy is resolved for these cryptic lineages of conservation concern, so conservation of these species may occur. One of the major challenges for taxonomists in recent times has been the species delimitation of morphologically cryptic taxa. The detection of distinct molecular lineages within cryptic genera has increased exponentially over the past decades with advances in genetic techniques. However, there are discrepancies in the rate and success of detection of cryptic taxa between studies using genetic methods and those using classic external morphology analyses. Therefore, novel integrative methods for species delimitation of cryptic taxa provide an avenue to incorporate multiple lines of evidence, including the application of osteological variation assessment where external morphological assessment fails to distinguish species. I develop a new pipeline integrating genomic data using single nucleotide polymorphisms (SNPs) and osteological geometric morphometric evidence from micro X-ray computed tomography (CT) imagery to assess variation between cryptic lineages for confident species delimitation. Here, I use this novel integrative pipeline to delimit cryptic lineages of earless dragons in north-eastern Australia. Prior to this study, there was evidence of three undescribed species of Tympanocryptis in this region. Using single mitochondrial and nuclear genes along with >8500 SNPs, I assess the evolutionary independence of the three target lineages and several closely related species. I then integrate these phylogenomic data with osteological cranial variation from CT imagery between lineages. I find that the very high levels of genomic differentiation between the three target lineages is also supported by significant osteological differences between lineages. By incorporating multiple lines of evidence for species delimitation, I provide strong support that the three cryptic lineages of Tympanocryptis in north-eastern Australia warrant taxonomic review. Earless dragons are found in most environments across the Australian continent, including a variety of ecological niches, from stony desert to tropical woodland or cracking clay savannah, although each species is often restricted to s certain habitat-type. I investigate the phylogenetic relationships among currently described earless dragons and newly delimited putative species with an assessment of broad biogeographic divisions, focussing on the north-eastern Australian Tympanocryptis group. I found significant structure across the north-eastern Australian lineages, with deep divergence between lineages occurring in the inland Great Artesian Basin region and more coastal Great Dividing Range. Regional diversification is estimated to have occurred in the late Miocene with subsequent Plio-Pleistocene speciations, and divergence and distributions of these species may therefore be reflective of the climate induced grassland-rainforest oscillations during this time. Based on these phylogenetic geographic relationships and the species delimitation from the integrative taxonomy approach, I describe three new species of Tympanocryptis from the cracking clay grasslands of the Darling Riverine Basin (T. darlingensis sp. nov.) and Queensland Central Highlands (T. hobsoni sp. nov.), and the stony open eucalypt woodlands on the Einasleigh Uplands (T. einasleighensis sp. nov.). The revision of these species provides further taxonomic clarity within the Tympanocryptis genus, and is an imperative step in the conservation of the north-eastern Australian earless dragons. These three putative Tympanocryptis species and the other three recently described earless dragons in north-eastern Australia inhabit restricted niches and areas with varying levels of habitat fragmentation and modification, and are therefore of significant conservation concern. However, little is known about these six north-eastern Australian earless dragon species. I utilise genomic methods to investigate population connectivity and genetic structure to determine management units. I then use species distribution modelling (SDM) to assess habitat suitability and fragmentation of each species. I integrate results of these analyses to form conclusions on the distribution and population structure of these earless dragons. I then discuss the major threatening processes and potential conservation strategies. This thesis uses several integrative approaches in resolving the taxonomy and forming conclusions on the conservation management of the north-eastern Australian Tympanocryptis species. This study successfully delimits cryptic lineages, explores the phylogenetic and geographic relationships between species, and provides baseline population genomics and ecological data to be used for conservation assessments and management decisions of earless dragons in north-eastern Australia.
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ItemCost-effective methods in conservation( 2018)Conservation resources are scarce, whether it is time, money or effort. Therefore, wise spending is important and decisions need to be made on how to prioritise limited resources between different conservation actions. Effectively targeting declines in biodiversity requires monitoring and management, each of which contribute differently to improved conservation outcomes. Monitoring provides information about the system (whether it is about the state or the dynamics), while management aims to halt downward population trajectories. Often monitoring and management are competing for the same resources, creating trade-offs in how these resources should be spent. In this thesis, I examine trade-offs in conservation, by focusing on how alternative resource allocations within monitoring, and between monitoring and management, impact the ultimate conservation outcome. I illustrate this with two case studies: the endangered growling grass frog (Litoria raniformis) metapopulation around Melbourne, Australia, and the invasive yellow crazy ant (Anoplolepis gracilipes) on Christmas Island, Australia. The first chapter provides a general introduction to the role of monitoring and management in conservation and the trade-offs that exist within and between them. In the second chapter, I examine whether increasing the spatial coverage of a monitoring program for the growling grass frog can replace learning about metapopulation dynamics in terms of population persistence. The advantage of obtaining reliable estimates from spatial monitoring over temporal monitoring is that wasting invaluable time is avoided. In the third chapter, I explore management of the endangered growling grass frog metapopulation, and study how alternative resource allocations between monitoring and management affect the confidence about sufficient offsetting actions. Increasing urbanisation requires habitat offsetting to reduce further declines in the metapopulation. Investing in monitoring might result in more precise estimates of the metapopulation dynamics, and hence allow managers to be more confident about which management strategy might be best. More management, on the other hand, might reduce the extinction risk of the metapopulation directly, provided suitable actions are chosen. Determining the optimal allocation of resources between the two is important to ensure the metapopulation gains as much as possible from the implemented offsetting management. In the fourth chapter, I switch focus to an invasive species, the yellow crazy ant, and investigate how to optimally survey an island for high density super-colonies. I compare effectiveness of a survey strategy that explicitly accounts for the variation in survey cost across the island with alternative ones that ignore survey cost estimates. In the fifth chapter, I determine the amount of monitoring data that contains sufficient information to find the ant super-colonies. Using a habitat suitability model for the super-colonies, combined with survey cost estimates, I prioritise sites, and evaluate the impact of more monitoring data on the amount of super-colonies found. Monitoring a small part of the island is sufficient to find the maximum possible super-colonies for a particular budget, resulting in the effectiveness of the survey strategy levelling off. This suggests that the resources that are currently spent on monitoring the entire island, can be redirected towards management of the invasive species. Finally, in the last chapter, I summarise the main findings of this research and discuss some potential paths for future research.
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ItemTriple jeopardy in the tropics: assessing extinction risk in Australia's freshwater biodiversity hotspot( 2017)Freshwaters are the most degraded and imperiled ecosystem globally. Despite this high vulnerability, conservation efforts in freshwaters often lag behind those in terrestrial and marine ecosystems. In Australia this is particularly evident; despite high levels of river degradation, few freshwater fishes have had their conservation status assessed and only 14% of fishes are listed. Most listed species are restricted to southern Australia where rivers are particularly degraded. Northern Australia’s rivers are very diverse with many highly range restricted fishes. Yet almost no species are listed, despite potential vulnerability and an increasing number of threats across the north. Nowhere is this more evident than the Kimberley region in the north-west, where 49% of species are restricted to three or fewer rivers, and 10% are restricted to an area of <20 km2. Very little is known about the ecology of the region’s endemic fishes, so their vulnerability cannot be assessed. In my thesis I assess extinction risk in the freshwater fishes of the Kimberley using the triple jeopardy framework, that is whether they have small geographic ranges, low abundances and/or narrow ecological niches. Specifically I aim to (1) determine the relationships between range size, body size and abundance in all Australian freshwater fishes and (2) whether these relationships can be used to identify species at risk of extinction. I then determine whether (3) small ranged Kimberley endemics have narrow habitat, dietary or thermal niches compared to closely related widespread species and (4) synthesize these results to identify the fishes most at risk of extinction in the Kimberley. First, I test for a relationship between geographic range size and body size in all Australian freshwater fishes. I then investigate how this relationship varies with conservation status. I identify currently unlisted freshwater fishes that share traits with listed species and map their distribution, along with freshwater fish research effort, across Australia. I found a positive relationship between range size and body size. For a given body size, conservation listed species have a range less than one tenth the size of unlisted species. Based on this relationship, I identified 55 additional species that may be vulnerable to extinction. Most of these species are restricted to northern Australia where freshwater fishes are poorly known due to low research effort. Second, I test for abundance-geographic range size and abundance-body size relationships in Australian freshwater fishes and investigate how these relationships vary with conservation status. I identify and map currently unlisted freshwater fishes that are numerically rare, and combined with the results outlined above, map species with a double jeopardy risk of extinction. I found a negative body size-abundance relationship and no correlation between range size and abundance. Although relative abundance was a poor predictor of current conservation listing, I identified 59 consistently rare species. Twenty of these species (34%) currently suffer a double jeopardy risk of extinction and all were restricted to northern Australia. Third, using closely related widespread and endemic congeneric pairings of Kimberley freshwater fishes, I investigate whether endemic species have narrow dietary niches at any stage during their development. Using qualitative measures of habitat and presence/absence data, I also assess habitat specialization. Most range-restricted species have narrower ecological niches making them more vulnerable to extinction. Fourth I test the thermal performance of two pairs of congeneric species that are sympatric in the Drysdale River, with one widely distributed species and one range restricted species in each pair. In the Syncomistes pair, resting metabolic rate (RMR) was similar between species at low temperature but at higher temperatures the RMR of the widespread species was lower due to the onset of anaerobiosis. The range-restricted Syncomistes also has a higher critical thermal limit (CTL). In the Melanotaenia pair, the results were the opposite, with the widespread species having a higher CTL and RMR. The thermal performance of each species was related to their distribution within the catchment rather than their geographic range size, with the thermally sensitive species dominating the cooler, perennial downstream reaches, and the hardier species being more abundant in the hotter, more ephemeral upper catchment. Finally, I use the above information to assess the triple jeopardy extinction risk in the fishes of the Kimberley. Seventy-nine per cent of Kimberley endemic fishes are vulnerable on one or more axis, and two species had a triple jeopardy risk of extinction. The majority of vulnerable species are found in the remote rivers of the north-western Kimberley, but the most imperiled species (Hypseleotris kimberleyensis) is restricted to the heavily degraded Fitzroy River. My thesis shows that, despite fundamentally different environments, life histories and dispersal capacity, Australian freshwater fishes exhibit range size, body size and abundance relationships largely similar to terrestrial fauna. By identifying northern Australia as a hotspot of unrecognized vulnerable species, I provide an important context for guiding targeted research and informing future conservation management of Australia’s freshwater fishes. Combined with their small ranges and/or low abundance, the narrower niches of most Kimberley endemic species makes the region’s fishes particularly extinction prone. By identifying which endemic species are most vulnerable, my study provides specific information for targeting conservation efforts in the region. As the Kimberley and northern Australia more broadly are earmarked for major development, substantial effort is needed to effectively manage fish populations, design and manage developments with the environment as a major stakeholder and preserve remote rivers with high endemism and extinction risk. However, as northern Australia’s rivers are in good condition, with planning and research there is an excellent opportunity for proactive, properly informed freshwater conservation across the region.
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ItemRobust prediction and decision strategies for managing extinction risks under climate change( 2016)Effective management of biodiversity requires decision strategies that are robust to the uncertainty embodied in predictions of habitat suitability and environmental change. This is particularly relevant in the context of climate change, which may interact with existing threats in unexpected ways. Predictive modelling has become important for addressing questions about climate change impacts. In particular, correlative species distribution models (SDMs) are popular for predicting species' fates, and have been noted as effective tools for guiding conservation decisions. However, SDM predictions are uncertain due to our imperfect understanding of the processes underlying species-environment associations, and, crucially, imprecision in predictions of regional climate change. While this is widely recognised, SDM prediction uncertainty is frequently overlooked, and practical approaches to handling this uncertainty are rare. When SDMs are used to investigate questions of species' persistence during times of environmental change, failure to consider uncertainty about the arrangement and quality of habitat may lead to flawed inferences and ineffective management. It is therefore essential that we improve our understanding of key uncertainties, and develop methods that explicitly handle uncertainty in a way that promotes sensible management decisions. In this thesis, I explore these issues through case studies of the mountain pygmy-possum, Burramys parvus, in the alpine region of south-eastern Australia. I draw on a range of quantitative tools and classical decision theory to: (1) determine the magnitude of uncertainty about habitat suitability due to SDM predictor choice, and how this varies under climate change; (2) develop a framework for identifying the optimal spatial allocation of resources for species' conservation under climate change, given uncertain predictions of habitat suitability; (3) explore the utility of abundance time series for improving our understanding of environmental dynamics influencing populations; (4) combine SDMs and models of population dynamics with decision theory to assess the extent to which predictions are refined by explicitly including population processes; and (5) develop a suite of open source software tools that facilitate common ecological modelling tasks, making rigorous investigation of climate change questions more computationally efficient and feasible. I found that standard approaches to model evaluation obscure key differences amongst competing SDMs, suggesting that consideration of ecological relevance during model construction is essential. I showed that despite extensive uncertainty about future habitat, conservation actions can be prioritised in a way that reflects managers' appetites for risk and reward. I demonstrated that for spatially-structured populations, hierarchical models can reveal the spatial scales at which environmental processes control population growth. Regional synchrony in population dynamics is evident for B. parvus, but local, density-independent environmental forces are more important in determining abundance trajectories. Finally, I demonstrated that habitat change is an unreliable surrogate for a species' response to climate change. Predictions about the distribution and quality of future habitat for B. parvus are uncertain. However, this is an inevitable challenge when forecasting species' fates. Importantly, it does not preclude effective management. The way forward is to recognise and account for uncertainty in ecological models, thereby enabling sensible conservation decisions for species impacted by climate change.
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ItemAssessing and managing interacting species at risk of coextinction( 2016)Interactions between organisms are ubiquitous: predators hunt prey, plants compete for light, and pollinators visit flowers to forage on nectar. Through their interactions species influence each other's population dynamics and ultimately their persistence: Darwin was already convinced that if bumblebees became extinct their food plants would follow quickly. Despite their importance, interactions are commonly ignored when we assess species' extinction risk or plan for their conservation management. My thesis is divided into six chapters, addressing two important components of conserving interdependent species. First, I assess if and how we can use a common type of data - observed interaction networks - to assess the coextinction risk of interacting species in networks, and to predict how interactions influence cascading extinctions when interdependent species are lost. Secondly, I investigate how interacting species can be protected in combined management approaches, focussing on the increasingly common method of translocating species for conservation. To answer this questions, I develop a range of statistical and mathematical modelling approaches and apply these to theoretical simulations and empirical data. In chapter 2, I investigate how quantitative methods can help to identify those species in interaction networks that are at risk of coextinction, while incorporating important factors such as uncertainty and imperfect detection of species in the field. I develop a hierarchical $N$-mixture model that accounts for imperfect detection and allows one to disentangle two factors that influence interaction frequencies between species: the probability that two species interact, and the abundances of species. This enables one to estimate with uncertainty the number of interaction partners of a species and the community size of dependents. I fit the model to data that from simulations of different parameter scenarios and to empirical networks of flower-visiting insects found on a threatened ecological community of plants from the Stirling Ranges National Park in Western Australia. In chapter 3, I extend this modelling approach to investigate how imperfect detection and uncertainty influence the progression of extinction through mutualistic networks. Therefore, I apply the modelling approach from chapter 2 to observed networks to correct these networks for sampling bias. Then, I sequentially remove plant species from the networks to investigate how extinction cascades differ between observed and corrected networks. I show that networks corrected for sampling bias, are more densely connected and the interactions between species are more diffusely distributed throughout the networks. This causes corrected networks to be less specialised, and plant species to be more redundant, leading to increased network robustness. The results of chapter 2 and 3 indicate that imperfect detection strongly affects observed interaction networks and suggests that it is unwise to draw strong inferences for the conservation status of species and the robustness of ecosystems without acknowledging imperfect detection and uncertainty. In the second part of this thesis, I investigate management actions for improving the persistence of cothreatened interacting species, with a particular focus on conservation translocations. The fourth chapter investigates how useful current single-species translocation guidelines are for conserving cothreatened species and the interactions between them. I first classify potential systems of cothreatened species and devise appropriate management options for each system. Secondly, I extend current single-species guidelines to incorporate interactions in the assessment, planning and implementation phase for the conservation of multiple interacting species. For each phase of a translocation, I present case studies of threatened interacting species where a combined translocation could save the species. In chapter 5, I examine in detail how different types of interactions influence the optimal size of founder populations and the order in which interacting species should be translocated. I use mathematical models for coupled two-species systems, in which species interact in consumer-resource, competitive or mutualistic interactions. While some common rules in translocating interacting species emerge, most decisions about necessary founder sizes and translocation order are interaction-type specific. In the two chapters about combined translocations of cothreatened species, I show that interspecific interactions are important processes that shape population dynamics, and should therefore be incorporated into the quantitative planning of multi-species translocations. Finally in chapter 6, I synthesise the findings of my work and highlight future research avenues.
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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.