School of BioSciences - Theses
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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.