School of BioSciences - Theses
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ItemSpeciation and secondary contact in a colourful agamid, Ctenophorus decresii( 2019)Colour polymorphism, the co-existence of multiple heritable colour morphs within an interbreeding population, is thought to promote rapid phenotypic evolution and speciation. This is based on the importance of colour signals in reproductive isolation in combination with the underlying genetic architecture of polymorphism, where morphs are predicted to be governed by few genes of major effect. This prediction is supported by empirical data and stems from how colour morphs often differ in suites of co-adapted traits. During secondary contact between populations that differ in morphs, there is expected to be a high probability of genetic incompatibilities between morphs due to a breakdown of adaptive genetic correlations. Furthermore, colour signal divergence may also be accompanied by changes in behaviour and/or mating preferences leading to incompatibilities between populations which differ in morphs. These factors together may facilitate the formation of reproductive isolation and ultimately lead to speciation. In this thesis, I investigated divergence and the outcome of secondary contact between lineages of the tawny dragon, Ctenophorus decresii, which differ in morph number and type. Ctenophorus decresii is a sexually dimorphic agamid lizard endemic to South Australia, and comprises two genetically distinct and geographically structured lineages: northern and southern. I tested for differences in colour vision between the lineages, which differ in a sexual signal, male throat coloration, particularly in the absence or presence of ultraviolet (UV) reflectance. The northern lineage is colour polymorphic with four discrete throat morphs which lack significant UV reflectance: orange, yellow, orange-yellow (orange centre surrounded by yellow), and grey. Southern lineage males are monomorphic with blue throats and a strong UV reflectance peak. Male throat coloration is an important intraspecific sexual signal, as it is emphasised in territorial and courtship displays. I investigated whether lineages differ in visual sensitivity to UV wavelengths by measuring retinal opsin protein expression of four cone opsin genes (SWS1, SWS2, RH2, LWS) using droplet digital PCR. I found that lineages did not differ in gene expression of the four opsins and discussed this in the context of conserved visual sensitives in terrestrial systems. The lineages meet in a contact zone where multi-locus genetic data suggested the presence of hybrids and potential barriers to gene flow. Using extensive field surveys, male phenotype data, genomic single nucleotide polymorphisms (SNPs), and a mitochondrial (mtDNA) marker, I investigated the outcome of secondary contact between the lineages. Furthermore, I captive-bred pure and first generation (F1) hybrid offspring to characterise colour traits independent of exogenous selection. I found that the contact zone is narrow and several generations old with no parental forms or F1 hybrids present. The northern mtDNA haplotype was prevalent in hybrids, and there were high frequencies of backcrossing to the northern lineage but not to the southern lineage, indicating genetic incompatibilities. The northern throat polymorphism was maintained, without any loss of morphs, whereas the southern throat morph was absent. This contrasted with the more intermediate throat phenotype of captive-bred F1 hybrids, particularly in ultraviolet reflectance, suggesting strong selection for the northern throat phenotype within the contact zone. The viability and fitness of F1 hybrids have consequences for contact zone dynamics, and ultimately whether species boundaries are eroded or maintained. I performed pure and reciprocal cross F1 hybrids in a laboratory setting and measured parental reproductive traits and offspring fitness traits. I found that northern females have a higher reproductive output with more, larger clutches per breeding season and lower embryonic mortality. Although pure and hybrid offspring did not differ in individual fitness traits, hybrids produced from a combination of northern females and southern males exhibited higher fitness in more categories (i.e. growth rate, bite force, sprint speed). These factors in combination may contribute to the prevalence of northern lineage mtDNA haplotypes in the contact zone. Finally, I taxonomically separated the northern and southern lineages of C. decresii sensu lato on the basis of differentiation in morphology and male coloration, genetic divergence with restricted gene flow, and geographic structuring. This revision results in C. decresii sensu stricto (previously southern lineage) and C. modestus (previously northern lineage). I evaluated morphological traits of the type specimen of Amphibolurus modestus (Ahl 1926), previously a synonym of C. decresii sensu lato, and determined that it represented a specimen of the northern lineage. Therefore, I formally re-instated and re-described Ctenophorus modestus (Ahl 1926). The addition of this species to the C. decresii species group, which now comprises six species, supports the notion that geographic divergence in male coloration is an important component to speciation in this group.
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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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ItemHeterozostera resilience( 2019)Seagrass perform critical provisioning, regulating, cultural and supporting ecological functions and services humans rely on worldwide. Unfortunately, many seagrass ecosystems are vulnerable to disturbance and are being lost at alarming rates. Some seagrass species have been listed by the International Union for the Conservation of Nature as threatened and endangered where population sizes are small or are highly restricted in geographic distribution. For several other species, there is not enough data to determine whether a species is at risk or not. When ecological resilience thresholds for species survival and reproduction are exceeded, declines in seagrass may occur. Declines over time and space may be episodic or ongoing and occur as a result of impacts from both natural and anthropogenic stressors, such as turbidity, eutrophication, hypersalinity and urbanization. Increasing global change phenomena are expected to exacerbate declines of seagrass in many parts of the world, and vast losses of seagrass have functional implications for other ecosystems and organisms. Heterozostera are unique seagrass broadly distributed throughout coastal southern latitudes especially in Australia. Only three populations of Heterozostera are found outside of Australia, in a small region of the eastern Pacific in Chile. The populations are made up of 2 nonflowering clones. Therefore, Heterozostera of Australia may be functionally endemic to southern Australia, including Tasmania. Substantial loss of Heterozostera has been reported from the middle of Heterozostera's range in several locations of Victoria, Australia. Subsequent recovery of diminished populations has been slow in some sites, especially in Western Port, Victoria. Few published accounts related to resilience, including seagrass population monitoring for conservation and restoration of Heterozostera in the southern hemisphere have been completed. The aim of this thesis is to advance basic botanical research on Heterozostera in support of taxonomic resolution and the development of conservation strategies, especially those focused on modeling and applied seagrass resilience and restoration in Australia. More studies are needed to contribute to the development of restoration and resilience management strategies for lesser studied southern hemisphere seagrass ecosystems, and this work supports the generation of additional discoveries. Specifically, the objective of this dissertation is to identify and examine the autoecology and resilience Heterozostera, including sexual and clonal reproductive success under variable environmental cues. In all, five comprehensive studies of Heterozostera biogeography and biology are included in this dissertation, along with a theoretical framework and summary exploring the roles of environmental parameters in the autoecology of resilience for temperate Australian Heterozostera. Chapter 1 presents a review of research in support of Australian Zosteraceae, including trends and gaps in our understanding of seagrass resilience mechanisms, including both resistance and recovery pathways in Heterozostera. Chapter 2 details the results of an extensive survey of existing sediment and nutrient conditions for Heterozostera populations across 15 seagrass meadows located in southeastern Australia's Port Phillip Bay. Chapter 3 summarizes a series of experiments aimed at discovering effective Heterozostera seed storage and collection protocols for use in land based aquaculture, and specifically examining the potential roles of seed colour, sterilisation and refrigeration with the goal of improving long term seed viability. Chapter 4 contains a fully factorial germination assay undertaken to identify potential cues to Heterozostera germination, including sediment type and sterilization, nutrient loads, and refrigeration. Chapter 5 details a germination experiment using a 2 ppm copper sulphate (CuSO4) solution to cue germination of Heterozostera seed. Lastly, Chapter 6 explores the rates of asexual growth and survival of three types of clonal reproductive Heterozostera propagules (rhizome, plantlet and shoot). This work provides novel information about several topics of research with regard to the autoecology of Heterozostera including: (1) species identification, (2) species ecology and biogeography, (3) reproductive material collection and storage, (4) seed germination, and (5) clonal transplanting. This research demonstrates Heterozostera is capable of widespread recovery across a range of sediment and nutrient conditions. Continued work on lesser known Heterozostera species (H. tasmanica and H. polychlamys), and other rarer seagrasses world-wide are critical for understanding the potential loss of resilience and increased vulnerability (or conversely, the potential for recovery, adaptation and survival) of threatened and endangered seagrass populations with limited global dispersal. Collectively these studies details methods to support future Heterozostera research in both laboratory and field settings where culture of reproductive materials are required. In addition, the outcomes from this research provides novel information in support of progressing insitu seeding and transplanting efforts aimed to improve operation of land based seagrass nurseries and research studies. Novel evidence builds support that Heterozostera nigricaulis as a functionally resilient species of seagrass, largely due to its ability to inhabit variable ecological conditions and to utilize multiple sexual and asexual reproductive strategies to recover populations following disturbances.
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ItemPredicting ectotherm life cycles under a variable climate: physiological diversity of matchstick grasshopper eggs and their ecological and evolutionary implications( 2019)Understanding the processes underlying the phenology and distribution of species is a key problem in ecology. These relationships are important for predicting the responses to species to environmental change. Phenology and distribution are closely linked to climate and weather through the thermal dependence of life cycles. However, for many biodiverse taxa, like insects, we have a poor understanding of the mechanistic links between adaptive traits and how life cycles are adapted to seasonal and variable temperature patterns. Insect life cycles are synchronised with suitable climatic conditions at critical life stages, such as the egg stage. Variation in thermal sensitivity of development and dormancy are two mechanisms by which insects can generate adaptive life cycle phenotypes. Eggs, therefore, present a unique opportunity to link adaptive variation in traits with corresponding variation in life cycles and thermal environments to examine how life cycles are adapted to variable climates. To understand the adaptation of insect life cycles to variable climates, we require a mechanistic understanding of the interactions between adaptive developmental traits of eggs and variation in the thermal environment on adaptations. Our ability to test thermal adaptation in ectotherms is also limited by our ability to efficiently characterise thermal responses. In this thesis, I described how thermocyclers are an efficient means of characterising the thermal response of small ectotherms with enough precision and sample size. I then used the widely distributed, endemic and flightless Australian matchstick grasshopper genera Warramaba (Orthoptera: Morabidae) as a model system to examine the significance of variation in thermal responses at the egg stage for life cycles under a variable climate. I used a mechanistic modelling framework to tease apart developmental and environmental sources of variation in life cycles at the egg stage and simulate their consequences for phenology and distribution in the field. Matchstick grasshoppers showed remarkable diversity in developmental responses to temperature at the egg stage, primarily in the expression of dormancy. I found that diverse Warramaba life cycles are shaped by the interactions between such developmental variation and local environmental temperatures. I demonstrated that we can achieve a mechanistic understanding of life cycle adaptation by considering the evolution of temperature-dependent traits and the evolution of life history within the context of seasonal temperature cycles. Mechanistic models are powerful tools to investigate the sources of life cycle variation and their consequences for insect distribution and phenology. Such frameworks are directly transferrable to other socio-economically important or threatened species to understand how insects are adapted to local climatic conditions and predict responses to a changing climate.
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ItemWho to trust? Assessing and improving expert judgement in ecological domains( 2019)Managing ecosystems and species involves estimation and prediction of complex ecological interactions and their response to management intervention. While data are invaluable for informing management decisions, often the data required are unavailable, incomplete or uninformative. In these contexts, expert judgement is routinely utilised to inform critically important decisions. It is important that these judgements represent the best possible foundation for decisions and assessments. The application of structured expert elicitation protocols has been advocated as a means by which expert judgement may be improved. While these protocols have been substantially discussed in the ecological literature, their widespread application in ecological domains has remained limited. It is suggested that a lack of prescriptive guidance, supported by evidence that structured protocols can be applied within the practical and financial constraints of most ecological contexts, may be impeding the widespread adoption of these protocols. This thesis explores how barriers to the implementation of structured elicitation protocols may be overcome, and the extent to which their application improves judgements. It provides prescriptive guidance on the application of the IDEA protocol for structured expert elicitation, and presents evidence that the application of the entire protocol is both practical and improves judgements. It examines how judgements derived from the IDEA protocol may be further improved through performance weighted aggregations of the Classical Model, and the extent to which performance weighting may be practically applied.
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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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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.