School of BioSciences - Theses
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ItemMolecular systematics of siphonous green Algae (Bryopsidales, Chlorophyta)( 2018)The evolutionary history of the siphonous green algae (Bryopsidales, Chlorophyta) was investigated using a combination of molecular techniques and phylogenetic inference methods. Analyses of chloroplast genomes of the order revealed the high variability of genome architecture and intron content. Proliferation of nonstandard genes associated with mobile functions (i.e. reverse transcriptase/intron maturase, integrases, etc.) was also observed. Evolutionary relationships of families in the order were investigated by increasing taxon sampling and using chloroplast genome data. The chloroplast phylogenies provided good support for the suborders and most families. Several early branching lineages were also inferred in the Bryopsidineae and Halimedineae. A new classification scheme was proposed for the order, which included the following: establishment of the family Pseudobryopsidaceae fam. nov.; merger of the families Pseudocodiaceae, Rhipiliaceae, and Udoteaceae into a broadly circumscribed Halimedaceae and establishment of tribes for the different lineages found therein; finally, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on the chloroplast phylogenies. Plastid (tufA) and nuclear markers (HSP90) and morphological observations were employed to delimit the Halimeda species found in Western Australia. This facilitated the recognition of Halimeda cuneata and the reinstatement of Halimeda versatilis. Investigation on morphological complexity revealed that simple uniaxial thalli was the ancestral state of the siphonous green algae and was maintained throughout their early evolution. Complex multiaxial thalli evolved afterwards on independent occasions.
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ItemPhylogeny of Eremophila and tribe Myoporeae (Scrophulariaceae)( 2018)Myoporeae is one of eight tribes recognised in the large, cosmopolitan plant family Scrophulariaceae sensu stricto. Tribe Myoporeae contains seven genera, four of which are endemic to Australia (Calamphoreus, Diocirea, Eremophila, Glycocystis), and the remaining three are distributed in the Caribbean (Bontia); Southern China and Japan (Pentacoelium); and throughout Australia, islands of the Pacific, Hawaii and Mauritius (Myoporum). The largest of these genera, Eremophila, contains over 220 species and is a major component of Australia’s largest biome, the Eremean (arid) zone. A monograph of the tribe was completed just over a decade ago (Chinnock, 2007), which provided an extensive and comprehensive taxonomic framework from which to explore the relationships and evolutionary history of the group. The first phylogenetic study of the Myoporeae (Kelchner, 2003) used two chloroplast markers to better understand generic and species level relationships in the tribe, however, due to a lack of phylogenetic resolution, the results were inconclusive. The aim of this thesis was to generate a comprehensive molecular phylogeny of tribe Myoporeae, utilising the capabilities of high throughput sequencing (HTS) technology. A genome skimming approach was implemented using a custom in-house method of library preparation, to allow for inclusion of the large number of samples required for the study. All three plant genomes (chloroplast, nuclear, mitochondrial) were represented using the genome skimming method, allowing for comparisons to be made between phylogenetic analyses of each genomic dataset. Entire chloroplast genomes (cpDNA) were assembled for 317 taxa, resulting in a well resolved and highly supported phylogeny (see Chapter Three). All allied genera were found to be nested in a paraphyletic Eremophila, with high levels of support. Chinnock’s (2007) sectional classification of Eremophila was only partially supported, with many of the 25 sections scattered throughout numerous clades. For the majority of species included with more than a single sample, a lack of monophyly was observed, which is largely attributed to the effects of introgressive hybridization, incomplete lineage sorting, and/or inappropriate species boundaries. In Chapter Four the entire nuclear ribosomal cistron (nrDNA) was assembled for 355 taxa, then analysed to a produce a moderately supported phylogeny. This phylogeny was largely congruent with the morphology-based taxonomy of the group, though differed markedly from the cpDNA phylogeny of Chapter Three. From a generic perspective, all allied genera were still nested in a polyphyletic Eremophila, while Chinnock’s (2007) sectional classification was better supported by monophyletic lineages (though still in need of revision). An increase in species rank monophyly was also observed relative to the cpDNA analysis, indicating that at least for some species, introgressive hybridization is likely to impact the chloroplast phylogenetic signal. In Chapter Five the mitochondrial genome (mtDNA) was explored, and five regions selected for analysis across a subset of 31 taxa in Myoporeae. The size and prevalence of structural rearrangement within the tribe meant assembly of entire mitogenome(s) was not feasible. Regions selected for analysis displayed low levels of variation, allowing for a moderately well-resolved phylogeny, mostly congruent with the nuclear ribosomal phylogeny of Chapter Four. Overall, construction and comparison of the three genomes in this study allowed for robust interpretation and increased understanding of the complexity in the evolutionary history and phylogenetic relationships of taxa in tribe Myoporeae. Taxonomic revision is needed at generic and sectional levels; however these changes will not be undertaken until further nuclear sequence data allows the relationships of taxa at the basal nodes of the nuclear phylogeny to be resolved. Aside from future taxonomic work, it is anticipated that this study will inform new research on the tribe Myoporeae, including the chemistry of Myoporeae (for pharmacological application); the study of plant:insect interactions between Myoporeae and members of the insect family Miridae; and biogeographic study of Australia’s Eremean zone.
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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.