School of BioSciences - Theses
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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.
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ItemEvolution and biogeography of Australian tropical freshwater fishes( 2016)Australia’s freshwater fish fauna is the most depauperate of any continent (256 formally recognised species), although endemism is exceptionally high (74%), largely due to its arid climate and history of isolation from other land masses. The Australian Monsoonal Tropics (AMT) biome in the tropical north is an exception. The AMT encompasses 33% of the Australia landmass, but contains 65% of the Australian fish fauna and, in a global context, the biome and many of its catchments contain moderate to high species richness relative to their size. However, the biodiversity, evolution, and biogeography of the AMT’s fish fauna remain poorly studied relative to the rest of the continent. In this thesis I utilise samples from the most comprehensive region-wide collection of freshwater fish molecular and distributional data in the AMT to help answer three fundamental questions regarding the regions freshwater fish fauna: (1) what is the true biodiversity of the AMT; (2) what are the key evolutionary processes driving and maintaining freshwater fish diversity across the region, in particular the highly endemic fauna of the Kimberley bioregion; and (3) what are the key patterns in diversity and distributions across the landscape and how can they be arranged into a cohesive biogeographic framework? First, I conducted a multigene molecular assessment of species boundaries in the AMTs most speciose freshwater family (Terapontidae) in order to assess the phylogenetic relatedness of terapontids in northwestern Australia (including the Kimberley) to the level of population, and to identify any unique genetic lineages that likely represent undescribed ‘candidate species’. I demonstrated the presence of 13 new candidate species within the Kimberley, more than doubling previous estimates of terapontid diversity in the region. Second, I conducted an assessment of morphological (morphometric and meristic) data from seven of the genetically defined candidate taxa, and the four previously described species within the genus Syncomistes to see if the seven candidates can be discriminated morphologically and to determine which characters best delimit taxa. I found an impressive array of meristic and morphometric character differences between species within Syncomistes and determined that the head, particularly feeding structures such as the jaw and dentition, were the most important morphological features in discriminating between taxa. Third, I looked for congruence between phylogenetic patterns in Kimberley terapontids and both past (low sea-level)/present (high sea-level) geological barriers and pathways as identified by GIS analysis, and tested the general hypothesis that geographic isolation of terapontid lineages during Pliocene and Pleistocene high sea-levels triggered the onset of reproductive isolation between taxa thus driving rapid speciation in the region. I found that most Kimberley terapontid species arose during the Plio-Pleistocene glacial cycles and are at different stages of allopatric divergence and speciation caused by the same vicariant processes. The results support the hypothesis that changing sea levels during late Pliocene and Pleistocene glacial cycles are a key driver of speciation and distributional patterns in the Kimberley. Fourth, I combined phylogenetic, biogeographical and diversification analyses to examine the nature of the Kimberley as a mesic refugium. Specifically, I investigate the tempo and timing of endemic diversification to see if the Kimberley has been a ‘museum’ or a ‘cradle’ of diversification. My combined molecular clock estimates and likelihood-based historical biogeographic reconstructions suggest that terapontids recently transitioned into the Kimberley from the east during the late-Miocene. Outstandingly, ~80% of Kimberley terapontids diversified within the region in the last 3 Ma. Further diversification analyses identified a single significant shift in diversification rates ~1.4 Ma that corresponds with a significant change in global climate midway through the Pleistocene. Given these finding my findings suggest that the Kimberley has been acting as a cradle of Neoendemism. Fifth, I generate a bioregionalisation of the freshwater fish in the AMT using the Simpson’s beta dissimilarity metric, and then assess the relationships of the biogeographic regions to their current environment using generalised dissimilarity modeling (GDM). I also estimate true species richness across catchments using the Chao 2 index in order to identify major sampling gaps. I propose three major freshwater fish bioregions and 14 subregions that differ substantially from the current bioregionalisation scheme. I found that species turnover was most strongly influenced by environmental variables that reflect changes in terrain (catchment relief and confinement) and productivity (NPP and forest cover). Current river orientation and historic connectivity between rivers during low sea-level events also appear to be influential. Three focal points of species richness and two of endemism were identified in the AMT, considerably expanding upon the spatial understanding of these patterns. Finally, a number of key sampling gaps are identified that need to be filled in order to fully refine the proposed regionalisation. Overall the results of this thesis add considerably to biodiversity estimates and the taxonomic knowledge of freshwater fish communities in the AMT. It also helps determine the major drivers of speciation in the Kimberley, the mode of diversification, and provides insight into the regions function as an evolutionarily important mesic refugium. Finally, it provides a modern freshwater bioregionalisation of the AMT and helps to determine the environmental variables driving community change across the landscape. These findings have important ramifications for the conservation of Australia’s tropical freshwater fishes. The Kimberley in particular is highlighted as not only an important evolutionary refugium, but also as a catalyst for narrow range endemic speciation. As a result the regions contains some of the most threatened freshwater fish communities in Australia.
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ItemPhylogeny and phylogeography of Zieria (Rutaceae)( 2016)Zieria (Anthophyta: Rutaceae) is a predominately Australian genus of shrubs and small trees, consisting of 59 Australian species and one species endemic to New Caledonia. Although there has been considerable taxonomic revision of this genus in recent decades, largely based on morphology, a comprehensive molecular phylogenetic study that would include as many currently-recognised taxa as possible was clearly needed. Using five chloroplast markers (rpl32–trnL, trnL–F, trnQ–5'rps16, trnS–G and 3'trnV– ndhC) and two nuclear DNA markers (ITS and ETS) this study undertook phylogenetic analyses in order to understand relationships, evolutionary processes and taxonomic issues in Zieria, and to interpret biogeographic patterns. Both Bayesian inference and maximum parsimony methods were employed. Almost all species of Zieria were represented in separate analyses of the cpDNA and nrDNA datasets, with the monotypic sister genus Neobyrnesia used as the outgroup. The results show that relationships within Zieria are complex; widespread incongruence was revealed between cpDNA, nrDNA and currently recognised taxa. A combination of factors is suggested to explain this, including regional cpDNA introgression (chloroplast capture) and incomplete lineage sorting, and the need for taxonomic revision of some taxa. The nrDNA provided greater support for monophyly of species than cpDNA, and potentially a better indication of phylogeny. However, deeply divergent paralogues of nrDNA were detected in some taxa, making the assessment of phylogenetic relationships more challenging, and highlighting some possible pitfalls in using nrDNA for phylogenetic reconstructions. The phylogenetic relationship of Australian taxa and Z. chevalieri, the single endemic New Caledonian species, is of particular interest in terms of the long-standing debate over the history of New Caledonia and its flora. The placement of Z. chevalieri differed between cpDNA and nrDNA trees. The cpDNA phylogeny placed Z. chevalieri as sister to all other species in the genus, suggesting that the earliest divergence was between lineages of New Caledonia and Australia, and that differentiation of species occurred through vicariance. In contrast, Z. chevalieri was placed higher in the nrDNA tree, which could suggest later dispersal, over water or via past exposed land in the Tasman Sea rather than older vicariance between Australia and New Caledonia. However, the results did not favour one hypothesis over another, and the debate will continue. A phylogeographic study of one widespread species, Zieria arborescens, was also undertaken, focusing on populations in the wet forests of Victoria and Tasmania. The cpDNA was not highly informative but provided some evidence of Tasmanian–eastern Victorian connections, interpreted as past geographic connectivity during periods of low sea-level now severed by Bass Strait. Finally, a number of taxonomic issues arising from the results of this project are discussed, and recommendations are made for reappraising and possibly re-circumscribing several taxa. In some cases this might require the description of new species based on variation between populations (e.g. Z. smithii and Z. furfuracea), or recircumscription of taxa to effect monophyly (e.g. Z. arborescens). Some taxa might be considered conspecific based on noteworthy similarities of morphological and genetic characters (as seen in this study) and the geographic proximity of populations (e.g. Z. buxijugum and Z. parrisiae; Z. alata and Z. madida; Z. verrucosa and Z. vagans; Z. caducibracteata and Z. arborescens; and Z. minutiflora and Z. obovata).