School of BioSciences - Theses
Permanent URI for this collection
Search Results
1 - 3 of 3
-
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.
-
ItemMacro-evolution in brittle stars( 2018)Conspicuous large-scale diversity patterns and the disparity of species-richness across different taxonomic groups have fascinated naturalists for centuries. In recent years, advances in molecular techniques have facilitated the generation of large amounts of genetic data and have permitted the investigation of long-standing macro-evolutionary questions in a phylogenetic framework, even when the fossil record is scant. With the deep-sea being largely unexplored, many questions remain unanswered and processes affecting diversity in the oceans are far less understood than in terrestrial or aquatic ecosystems. Brittle stars have become a great model to study evolutionary processes, as an extensive genomic dataset has been generated. In this thesis, I aimed to identify large-scale diversity patterns in the oceans and to investigate their underlying processes in a phylogenetic framework. I used this extensive dataset, global distributional records, and novel phylogenetic approaches to investigate major processes at global scales. I investigated the dynamics of bathome shifts and the role of the deep-sea in generating diversity. The findings of bathymetric ranges being highly conserved, and shifts being infrequent, served as a baseline for the other chapters where evolutionary processes were investigated within bathomes. I also investigated the effect of the emergence of biogeographic barriers in shaping diversity patterns of tropical, shallow-water brittle stars. The temporally and spatially concordant divergences of clades, concordant across families, evidenced the role of plate tectonics in shaping spatio temporal patterns of diversity. Similarly, the role of geological processes in the evolution of the fauna of southern Australia was investigated. Three major components have been identified for this fauna, which are the result of geological and historical processes. Recent colonisations, either from tropical species colonising higher latitudes or temperate taxa dispersed from other regions in the Southern Ocean, have been identified based on fossil evidence. However, although a Gondwanan component has been suggested, fossils from the late Cretaceous are scarce, limiting our knowledge about the effect of the break-up of Gondwana. Revisiting this question using one of the most complete metazoan phylogenies to date reaffirm the important role of the Antarctic Circumpolar Current (ACC) in shaping diversity patterns in the Southern Hemisphere, but also of the break-up of Gondwana. Lastly, I investigated colonisations of anchihaline environments. Although several marine taxa have cave-adapted lineages, only three brittle stars have been reported to occur in these environments. As, these species belong to different families, they must represent independent colonisation events. I used evidence from multiple loci to perform species delimitation using robust methods, and assessed models of origin of cave fauna in a phylogenetic framework, considering life-history traits, and demographic history for the cave population. The questions addressed in this thesis evidence the power of phylogenomic approaches that in combination with extensive distributional datasets, shed light into macro-evolutionary processes. The results presented herein contribute and advance our knowledge about diversity and evolutionary processes in our oceans, and provide a framework for future research.
-
ItemComparative phylogeography and diversity of Australian Monsoonal Tropics lizards( 2016)Tropical savannah biomes cover ~20% of the world’s landmass, however the biodiversity encompassed within these environments and the underlying processes that have shaped it remain poorly understood. Recent increased research to address this knowledge gap have begun to reveal surprisingly high amounts of deep, geographically-structured diversity, much of which is cryptic or hidden within morphologically similar species complexes. These patterns are especially emphasized in vertebrate taxa which are intrinsically linked to rock escarpments and ranges that dissect the savannah woodlands and grasslands of many of these biomes, hinting at a role of heterogeneous topography in structuring diversity. The remote Australian Monsoonal Tropics (AMT) spanning the north of the Australian continent is a particularly vast, and relatively undisturbed, tropical savannah region. Recent increased surveys are revealing numerous new species and endemism hotspots, indicating we are only just beginning to uncover the true biodiversity levels within this biome. Not only is there a relative paucity of knowledge regarding the present diversity within this region, but there is also limited understanding of how this diversity came to be. Phylogeographic studies can assist us in establishing current patterns of diversity and their evolutionary significance within regions and biomes. Furthermore, by comparing and contrasting the patterns and timing of diversification within and between biomes for multiple ecologically diverse taxa, we can begin to elucidate the history of these biomes and the environmental processes that have shaped the diversity we observe today. In this dissertation I aimed to better assess and establish true patterns of biodiversity and endemism within the Kimberley region of the AMT (Western Australia), and to place these patterns within a broader continental context using intra- and inter-biome comparisons in related taxa. Using geckos as a model system I took a comparative phylogeographic approach, integrating advanced next-generation genetics and morphology to establish patterns and timing of diversification across ecologically variable taxa. Within all Kimberley taxa I studied, I uncovered high levels of cryptic diversity. Much of this diversity involves especially short-range endemic lineages concentrated in key regions typically with one or more of the following factors: highly mesic conditions, island or insular environments, and unique or complex geological formations. In recognising these areas I have provided evidence of novel biodiversity hotspots and emphasised the significance of others as representing important “refugia” within the Kimberley that allow persistence and facilitate divergence of lineages through harsh periods of environmental change. These findings indicate diversification patterns are shaped by complex interactions of climatic variation, topography, and species’ ecology, allowing inference of biogeographic history and a greater ability to predict impacts of future environmental change.