School of BioSciences - Theses
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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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ItemFrom little things big things grow - savanna burning, suppressed trees and escape from the fire trap in Australian mesic savannas( 2017)This thesis explores growth responses and strategies of fire-suppressed trees in mesic savannas. Frequent fires are common to savannas globally, and cause most savanna trees to remain trapped as resprouts in the understorey by a cycle of topkill, where all above-ground parts of the plant are killed, followed by resprouting. Escape of suppressed resprouts from this fire trap is reflected in savanna tree community structure and composition. In this thesis, I contribute to the growing body of work from across the savanna biome that seeks to unravel the different effects of fire, competition and species growth strategies as mechanisms driving savanna tree communities. This question is fundamental to understanding what limits tree biomass in savannas and to predicting effects of different fire regimes in both the short term and in future climate scenarios. Despite much argument and modelling, mechanistic drivers of mesic savannas remain topics of conjecture, in part due to historical, environmental and species trait differences between continents. I collected the data used throughout this thesis within the Tiwi Carbon Study, a nine-year long fire experiment that aimed to provide accounts of carbon stored in soils, live vegetation and dead biomass under different fire regimes. The carbon economy is becoming a significant economic contributor to Aboriginal communities across remote northern Australia, with associated human benefits of social empowerment, wellbeing and connection to traditional practices. The increased focus on active management of northern Australian savannas for carbon sequestration and emissions abatement within a carbon market provides a human perspective to the ecological focus of my thesis. Within this context, there is a renewed imperative to understand what limits trees in savannas to anticipate effects of changes to fire regimes on carbon stocks and biodiversity. Using individual-level data I collected for 11 common resprouting savanna tree species subjected to different fire regimes on the Tiwi Islands in monsoonal northern Australia, I: (1) develop a theoretic framework that describes persistence and escape of suppressed resprouts subjected to frequent fire; (2) develop novel methods for estimating species and fire-specific escape heights; (3) model resprout growth and escape from the fire trap as mediated by fire and competition; (4) define sapling growth strategies based on functional and architectural traits that may influence escape potential; and, (5) demonstrate the effects of varying fire frequencies on savanna structure and composition. I found that the likelihood of escape from the fire trap is context-specific and related to differences in fire intensity, species traits and topkill-avoidance. Fire promotes fast growth of trees compared to fire exclusion, which may promote higher escape rates over shorter timeframes. However, less frequent fire leads to increased midstorey densities overall, thus affecting stand structure. In Australian savannas, eucalypts receive particular attention because of their canopy dominance, but I found minimal evidence of distinctly different growth responses between eucalypt and non-eucalypt resprouts that might explain this. Fine-scale environmental variation and individual species characteristics must be considered for robust estimates of escape from the fire trap. My research further implicates non-fire disturbances and different reproductive strategies as potentially illuminating drivers of different species responses – important topics for future research.
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ItemThe ecological costs and benefits of urban stormwater wetlands to frogs( 2018)The speed and scale at which humans are altering natural systems creates novel challenges for many species. Some species can cope with human-induced rapid environmental change by exhibiting adaptive behavioural or phenotypic plasticity. Many others, however, respond maladaptively in ways that can impact individual fitness. When rapid environmental change triggers mismatches between perceived and actual habitat quality, animals can prefer inferior habitats, that are known as ecological traps. Using a meta-analysis, I show that ecological traps are an unexplored but potentially important conservation risk to animals within wetland habitats (Chapter 2). Focusing on urbanisation and stormwater wetlands as a case study, I assess how anthropogenic environmental change affects frogs, in terms of the environmental variables influencing species occurrence (Chapter 3), the capacity of individuals to make adaptive habitat selection decisions (Chapter 4), and the fitness and behavioural consequences of these decisions (Chapter 4 and 5). I show that frogs occupied wetlands across a broad spectrum of pollution levels, including even the most contaminated, and that pollution exposure reduced survival and impaired predator avoidance behaviours. Breeding frogs did not avoid wetlands where these fitness reductions occurred, demonstrating that stormwater wetlands can function as ecological traps. Collectively, my results highlight the need for a greater focus on individual-level metrics (e.g. fitness and habitat preferences) in addition to the more commonly measured population- and community-level metrics (e.g. richness and abundance). Based on my research, I propose three key recommendations to maximise biodiversity at wetlands within urban landscapes. Firstly, appreciate that poor water quality at stormwater wetlands may impact resident wildlife, and attempt to reduce the causal factors. Second, despite this, do not ignore the potential value of stormwater wetlands in providing habitat and enhancing connectivity amongst aquatic habitats, particularly when they are appropriately designed and managed. Finally, it is important to design and construct wetlands for wildlife that are not connected to stormwater networks, with their placement within the landscape carefully considered.
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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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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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ItemGeographic range and the mountain niche: ecology, adaptation and environmental change( 2015)The geographic range is one of the most fundamental traits of a species. For this reason, understanding the ecological and evolutionary drivers of the size, position, and structure of the range is a key research challenge. The geographic range also has an overriding influence on the environments to which a species is exposed and their spatial and temporal variation. This study addresses four questions relevant to understanding interactions between the environment and individuals, populations, species and communities, with a focus on mountain regions where environmental variation is particularly pronounced. First, using meta-analysis and a single-genus case study, I explore the relationship between geographic range size and characteristics of the ecological niche. Range size can vary by several orders of magnitude among closely related species, but is strongly and consistently associated with both niche breadth and niche position: the most widespread species tend to be those with a broader niche and/or those that utilise resources that are common across the landscape. Second, I investigate the relationship between niche and range limits by testing variation in physiological tolerance across environmental gradients in two mountain systems: beetles (Carabidae: Nebria Latreille) from the North American Cascade Range and grasshoppers (Acrididae: Kosciuscola Sjösted) from the Australian Alps. Whereas the Nebria, distributed across a 2000 m elevational gradient, showed almost no variation in thermal tolerance, the Kosciuscola showed significant interspecific variation in cold tolerance, consistent with the decrease in average temperature with elevation. I suggest that cold tolerance limits might constrain the upper range edge of at least one species. Third, I explore how past climate cycles and Australia’s dissected mountain landscape have influenced the population structure of an alpine-endemic grasshopper (Kosciuscola tristis) using a combination of genetic methods. Despite continuity of alpine habitat during Pleistocene glacial cycles and, by global standards, small-scale disjunctions in the present distribution of these environments, K. tristis showed deep lineage divergence associated with geographic breaks in alpine conditions. Fine-scale structure in the absence of clear geographic barriers suggests that habitat heterogeneity might structure populations at a regional scale. The last component of this work tests the response of alpine invertebrate species and communities to reduced winter snow cover. This is a likely future scenario in the Australian high country, where the winter snowpack is already marginal. I show that Australia has a diverse subnivean arthropod fauna, characterised by the high relative abundance of springtails (Collembola), mites (Acari), spiders (Araneae) and beetles (Coleoptera). Experimental reduction of the winter snowpack caused shifts in community composition, driven by a small number of abundant arthropod taxa. These effects were apparent at a small spatial and temporal scale, with rapid recovery from experimental perturbation in spring. Mountain ecosystems are threatened by climate change as they are already rare at a landscape scale, are typically fragmented and have limited scope for climate tracking. The work presented here highlights effects of small-scale environmental variation on species traits, genetic structure and communities, which could act to either buffer or exacerbate landscape-scale climatic changes.