Zoology - Theses
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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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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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ItemA predictive framework to assess response of invasive invertebrates to climate change: pest mite species of Australian grains( 2012)Climate change is set to place enormous pressure on both biodiversity and agricultural production. Important vectors of agricultural damage, such as pest invertebrates, are likely to respond to climate change in different ways. Differing pest invertebrate responses in grain crops will translate to shifts in outbreak frequency and persistence of pests, changes to pest species assemblages, and alter biocontrol by natural enemies. Successful management will thus require predictions of how climate change will affect individual species in terms of distributions and abundance. Climate change predictions for species are often based on models that characterize distributions though species-environment relationships. However, there are important factors relating to the ecology and evolutionary biology of species that are not incorporated and will mediate climate change response. This thesis aims to establish a transferrable framework, employing multiple, complimentary lines of enquiry, to build on distribution models and understand how climate change may affect different crop pests. I focus on two important mite species groups, the blue oat mites (Penthaleus spp.) and the redlegged earth mite (Halotydeus destructor). These mite species are invasive, and so understanding how they have adapted since being introduced into Australia will help predict response to climate change in the future. The first part of this thesis applies environmental niche models to distribution data of the three cryptic Penthaleus species, to make preliminary assessments of response to climate change. These models found that the distributions of each species are governed by different climate variables, and that species assemblages are likely to shift under climate change. The remainder of the thesis builds on such models by applying a more integrated approach to assess climate change response of H. destructor. This species provides an ideal candidate to develop this framework as the biology and ecology is well understood, and its introduction and spread in Australia has been well documented.