School of BioSciences - Theses
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ItemSystematics and biogeography of Spyridium with a focus on Spyridium parvifolium and its hybrids( 2022)Spyridium is a genus of c. 45 species endemic to south-western and south-eastern Australia, with a disjunct distribution across the Nullarbor Plain and Bass Strait. The genus also includes several morphologically distinct phrase name taxa. Spyridium parvifolium is a widespread and morphologically variable shrub from south-eastern Australia. Several varieties and forms of this species have been recognised, but there is disagreement on the accepted taxonomy between Australian states. Spyridium parvifolium is known to hybridise with S. daltonii in the Grampians and is thought to hybridise with S. vexilliferum in locations where these taxa co-occur in western Victoria and south-eastern South Australia. The aim of this research project was to develop a comprehensive molecular systematic understanding of Spyridium, and S. parvifolium and its hybrids, to inform the treatment of Rhamnaceae in the Flora of Australia (Kellermann et al. 2022-). The objectives were to investigate: the species circumscription and biogeographic history of Spyridium, the infraspecific taxa and phylogeographic patterns of S. parvifolium and introgression associated with this species (i.e. S. xramosissimum and S. parvifolium x S. vexilliferum). Entire chloroplast genomes (c. 160k base pairs) and the nuclear ribosomal array (18S–5.8S–26S; c. 6k base pairs) were analysed using both Bayesian and Maximum Likelihood phylogenetic methods. In total sequences from 230 samples were analysed across these phylogenies, including representatives of all recognised species of Spyridium, six phrase name taxa, seventy-two accessions of S. parvifolium, eight putative hybrids and four outgroup taxa. This study provides the most comprehensive phylogenies of Spyridium and S. parvifolium to date. For Spyridium, several biogeographic patterns were identified, including deep diverging clades of taxa endemic to Western Australia, New South Wales and Tasmania. Several taxa were identified as polyphyletic (e.g. S. eriocephalum and S. phylicoides), warranting taxonomical review. For S. parvifolium, early divergence of individuals from west of the Murray Darling Depression, isolation on the inland side of the Great Dividing Range and recent seed-mediated gene-flow across Bass Strait were identified in the chloroplast genome phylogeny. The variants of S. parvifolium were not supported as genetically distinct suggesting the infraspecific recognition of var. parvifolium and var. molle in Tasmania is not warranted. Molecular evidence of introgression between S. parvifolium and both S. daltonii and S. vexilliferum was identified, providing molecular support for hybrids also inferred from intermediate morphology. Other findings include inferred parentage, unidirectional introgression and recombination of the nuclear ribosomal array for some hybrid accessions.
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ItemPhylogenomics, molecular evolution and extinction in the adaptive radiation of murine rodents( 2020)Adaptive radiation plays a significant role in the generation of biological diversity, and the advent of modern sequencing approaches has unlocked a new genomic perspective on this process. Genomic-scale data from the across the diversity of adaptive radiations can provide unprecedented resolution of the phylogenetic, biogeographic and molecular context of diversification. Murine rodents (Murinae: Rodentia) are a recent and rapid adaptive radiation that make up > 10% of mammal species. Murines have repeatedly colonised new geographic areas and island systems in the Eastern Hemisphere, frequently as a result of overwater transitions. Recurring adaptive radiation, ecological character displacement, and convergent evolution across Murinae make them an ideal model for studying adaptive radiation, especially in the Indo-Australian region. Within broader Murinae, the Hydromyini are a speciose Australo-Papuan radiation that diversified following an overwater colonisation from Sunda to Sahul ca. 8 Ma. Previous multilocus studies did not provide sufficient phylogenetic resolution of the rapid diversification of Hydromyini, and did not adequately sample taxa to reconstruct their complex biogeographic history. In addition to unresolved biogeography, the endemic Australian clade within Hydromyini has suffered the highest rate of recent mammalian extinction in the world. The rapid decline of Australian rodents is thought to be primarily the result of predation by feral cats, combined with other factors such as anthropogenic land clearing. There is little information about the pace of decline in eight species that went extinct on the Australian mainland in the last 150 years, and it is unclear whether these species had suffered longer term declines that predate the arrival of Europeans into Australia in 1788. To resolve these outstanding issues, I develop a novel exon capture approach for murine rodents. Firstly, I investigate the degree of congruent and conflicting phylogenomic signal in a rapid radiation, using genus-level relationships in the Hydromyini as a model example. My results show that in a number of cases, strong conflict is not reflected in branch support metrics obtained using either maximum likelihood or summary coalescent approaches. This result is significant, as it suggests that approaches commonly used to estimate support in phylogenomic data can fail to detect uncertainty in the face of underlying genealogical heterogeneity. Further leveraging this novel exon capture design, I generate a robust phylogenomic tree based on > 350 samples across the Australo-Papuan continent, including extant and recently extinct species in Hydromyini. With these data, I reconstruct the species-level evolutionary and biogeographic history of the Hydromyini across Sahul, recovering numerous examples of overwater colonisation between regions. Consistent with the geomorphological hypothesis that the New Guinea lowlands emerged after the orogeny of the Central Cordillera, I find evidence for increasing ecological opportunity in the Hydromyini from approximately 5 Ma. This first species-level phylogenomic study spanning the entire Sahul region provides a baseline example for future comparative studies that seek to reconstruct the biogeographic drivers of diversification in Sahul at a continental scale. Using exon capture and whole-exome sequencing data from extinct and extant species, I place recently extinct Australian rodents in a phylogenomic context for the first time. I recover no marked evidence of genetic erosion in five extinct species at the time of specimen collection, in comparison to extant species with present-day low allelic diversity. This indicates that the decline of recently extinct Australian rodents occurred extremely rapidly, and its onset likely did not predate European settlement. Additionally, my results taxonomically resurrect a species from extinction, Gould’s mouse (Pseudomys gouldii), which survived as a single island population in Shark Bay, Western Australia (currently classified as P. fieldi). Finally, I generate whole exome data from 38 species in the global radiation of Murinae to examine patterns of positive selection and convergent evolution. I uncovered pervasive positive selection across genes associated with diet, digestion and taste across Murinae, and increased rates of adaptive evolution in carnivores compared to omnivores. Limited evidence for molecular convergence in worm-eating specialists Paucidentomys and Rhynchomys suggests a role for developmental phenotypic control in this striking example of ecological convergence. Broadly, my results indicate that the pronounced ecological and phenotypic shifts that are hallmarks of adaptive radiations may also drive corresponding shifts in the pace and pattern of molecular evolution across the genome. Together, the work in this thesis is fundamental to the understanding of diversification, adaptation and extinction in the Australo-Papuan region, and provides an extensive genomic resource for future studies.
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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.