School of BioSciences - Theses
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ItemSpeciation and secondary contact in a colourful agamid, Ctenophorus decresii( 2019)Colour polymorphism, the co-existence of multiple heritable colour morphs within an interbreeding population, is thought to promote rapid phenotypic evolution and speciation. This is based on the importance of colour signals in reproductive isolation in combination with the underlying genetic architecture of polymorphism, where morphs are predicted to be governed by few genes of major effect. This prediction is supported by empirical data and stems from how colour morphs often differ in suites of co-adapted traits. During secondary contact between populations that differ in morphs, there is expected to be a high probability of genetic incompatibilities between morphs due to a breakdown of adaptive genetic correlations. Furthermore, colour signal divergence may also be accompanied by changes in behaviour and/or mating preferences leading to incompatibilities between populations which differ in morphs. These factors together may facilitate the formation of reproductive isolation and ultimately lead to speciation. In this thesis, I investigated divergence and the outcome of secondary contact between lineages of the tawny dragon, Ctenophorus decresii, which differ in morph number and type. Ctenophorus decresii is a sexually dimorphic agamid lizard endemic to South Australia, and comprises two genetically distinct and geographically structured lineages: northern and southern. I tested for differences in colour vision between the lineages, which differ in a sexual signal, male throat coloration, particularly in the absence or presence of ultraviolet (UV) reflectance. The northern lineage is colour polymorphic with four discrete throat morphs which lack significant UV reflectance: orange, yellow, orange-yellow (orange centre surrounded by yellow), and grey. Southern lineage males are monomorphic with blue throats and a strong UV reflectance peak. Male throat coloration is an important intraspecific sexual signal, as it is emphasised in territorial and courtship displays. I investigated whether lineages differ in visual sensitivity to UV wavelengths by measuring retinal opsin protein expression of four cone opsin genes (SWS1, SWS2, RH2, LWS) using droplet digital PCR. I found that lineages did not differ in gene expression of the four opsins and discussed this in the context of conserved visual sensitives in terrestrial systems. The lineages meet in a contact zone where multi-locus genetic data suggested the presence of hybrids and potential barriers to gene flow. Using extensive field surveys, male phenotype data, genomic single nucleotide polymorphisms (SNPs), and a mitochondrial (mtDNA) marker, I investigated the outcome of secondary contact between the lineages. Furthermore, I captive-bred pure and first generation (F1) hybrid offspring to characterise colour traits independent of exogenous selection. I found that the contact zone is narrow and several generations old with no parental forms or F1 hybrids present. The northern mtDNA haplotype was prevalent in hybrids, and there were high frequencies of backcrossing to the northern lineage but not to the southern lineage, indicating genetic incompatibilities. The northern throat polymorphism was maintained, without any loss of morphs, whereas the southern throat morph was absent. This contrasted with the more intermediate throat phenotype of captive-bred F1 hybrids, particularly in ultraviolet reflectance, suggesting strong selection for the northern throat phenotype within the contact zone. The viability and fitness of F1 hybrids have consequences for contact zone dynamics, and ultimately whether species boundaries are eroded or maintained. I performed pure and reciprocal cross F1 hybrids in a laboratory setting and measured parental reproductive traits and offspring fitness traits. I found that northern females have a higher reproductive output with more, larger clutches per breeding season and lower embryonic mortality. Although pure and hybrid offspring did not differ in individual fitness traits, hybrids produced from a combination of northern females and southern males exhibited higher fitness in more categories (i.e. growth rate, bite force, sprint speed). These factors in combination may contribute to the prevalence of northern lineage mtDNA haplotypes in the contact zone. Finally, I taxonomically separated the northern and southern lineages of C. decresii sensu lato on the basis of differentiation in morphology and male coloration, genetic divergence with restricted gene flow, and geographic structuring. This revision results in C. decresii sensu stricto (previously southern lineage) and C. modestus (previously northern lineage). I evaluated morphological traits of the type specimen of Amphibolurus modestus (Ahl 1926), previously a synonym of C. decresii sensu lato, and determined that it represented a specimen of the northern lineage. Therefore, I formally re-instated and re-described Ctenophorus modestus (Ahl 1926). The addition of this species to the C. decresii species group, which now comprises six species, supports the notion that geographic divergence in male coloration is an important component to speciation in this group.
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ItemEvolution of drug-resistance genes in the asymptomatic Plasmodium falciparum reservoir of infection in Ghana( 2019)Ghana is one of the 11 countries in the world with the highest malaria burden. Like many other African countries, the majority of individuals of all ages harbour asymptomatic Plasmodium falciparum infections, which sustain malaria transmission. Yet these infections are largely undiagnosed and untreated. Chloroquine (CQ) was the main drug for treating clinical malaria in Africa until it was replaced with artemisinin-based combination therapies (ACTs) in the early 2000s due to treatment failures. At the same time, sulphadoxine-pyrimethamine (SP) was adopted for intermittent preventative treatment in pregnancy (IPTp). In order to inform future malaria control strategies in Ghana, I investigated the asymptomatic P. falciparum reservoir in Bongo District (BD), where malaria transmission is both high and seasonal. To evaluate the reservoir of asymptomatic P. falciparum infections including antimalarial drug-resistance markers in BD, a cross-sectional Pilot survey of ~700 participants (≥ 1 year) was undertaken at the end of the dry season in June 2012. Following the completion of this Pilot investigation a larger serial cross-sectional study (~2,000 participants) involving six seasonally timed surveys was completed between 2012 and 2016. This study was designed to evaluate the impact of indoor residual spraying with insecticides (IRS) on the prevalence and diversity of asymptomatic P. falciparum infections in BD before, during, and after the IRS intervention. At the end of the dry season in 2012 I showed that 38.3% of the population across all ages (1-85 year) carried asymptomatic P. falciparum infections. The majority (>70%) of these infections harboured CQ sensitive alleles (Pfcrt K76 and Pfmdr1 N86) and/or alleles associated with reduced response to SP (Pfdhfr I51R59N108/Pfdhps G437) and/or the ACT partner-drug, lumefantrine (Pfmdr1 N86F184). There was no evidence of selection of multilocus haplotypes (i.e. Pfcrt- Pfmdr1- Pfdhfr- Pfdhps) with predicted resistance to both CQ and SP, nor was there any evidence of artemisinin resistance based on Pfk13 genotyping. To further understand this rebound of CQ sensitivity in BD further analyses of the microsatellite loci flanking Pfcrt and Pfmdr1 indicated that the CQ sensitive alleles spread through the asymptomatic parasite reservoir via soft selective sweeps. They may have expanded from CQ sensitive lineages that survived CQ drug pressure, i.e. before Ghana switched to ACTs. Following the completion of the 3-rounds of IRS in BD, undertaken between 2013 and 2014, both the prevalence and multiplicity of asymptomatic P. falciparum infections among children (1-10 years) reduced significantly compared to the pre-IRS surveys. Interestingly, despite these reductions, parasite diversity as assessed by msp2 heterozygosity remained high and stable from the pre-IRS through to the post-IRS surveys. My findings suggest that the asymptomatic P. falciparum reservoir in BD poses a threat to malaria elimination and plays a role in the evolution of antimalarial resistance in Ghana. Therefore, strategies combining IRS with population-wide antimalarial treatments, potentially using ACTs with CQ, would have to be deployed and sustained in BD. Nonetheless, continuous monitoring of the molecular markers of resistance and for changes in the parasite diversity will be crucial to inform elimination strategies in Ghana and Africa.
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ItemThe function of female and male ornaments in the lovely fairy-wren( 2019)Ornaments like plumage colours or complex song are generally regarded as male traits that are shaped by sexual selection. By contrast, the factors that shape female elaborate traits have often been overlooked, though they are expressed in females across many taxa. Understanding how trade-offs and selective pressures shape female ornamentation is crucial for advancing our understanding of trait evolution. In this thesis, I investigate the form and function of female and male plumage colour and song in the Lovely fairy-wren (Malurus amabilis), a tropical species in which females and males are both highly colourful and vocal. This was investigated over three consecutive years and field seasons in Far North Queensland, Australia. My thesis research employed field observations, behavioural experiments, and genetic analysis, to test the adaptive function(s) and mechanisms for the evolution of female and male ornamental traits. I explicitly contrast females and males so that we can address, in the light of the abundant work done on males, how females may or may not differ from males. To provide context for the ornamental traits that are exhibited by this species, I first provide a comprehensive overview of the ecology and breeding biology of the Lovely fairy-wren, since a detailed description on the species natural history prior to this work was lacking. To understand the function of plumage colouration, I studied whether plumage colour in females and males is a signal and experimentally tested if it functions in a competitive context. Additionally, I assessed whether plumage colour is sexually selected, by examining its signalling content, costs (survival), and its relationship with reproductive and paternity success. Lastly, I investigated the song function, by describing female and male song structure and examining sex-specific variation in song rate across different contexts. I also used experimental data to examine female and male responses to simulated territorial intrusion. Overall this thesis provides insight into the form and function of both female and male plumage colours and song. First, it shows that visual and acoustic ornaments are important signalling components in different contexts, suggesting that female ornaments are not just a correlated genetic by-product of traits in males, and that selection favours female (and male) expression of traits. Second, the information conveyed by plumage colouration seems to be context-dependent in relation to the sex of the bearer: in males, it may follow the classical pattern of sexual selection, functioning in mate choice and male-male competition, while in females, plumage colours do not seem to be influenced by male choice, but function in same-sex competitive contexts. Third, it highlights that song has convergent functions in both sexes, as females and males have similar song structure and used song year-round in identical contexts for within-pair communication and joint territorial defence. The fact that females and males sing and have bright colours year-round in parallel with their territorial and breeding behaviour, suggests that individuals use their traits to maintain (sexual and non-sexual) resources. This work highlights the importance of studying and considering the fundamental differences in females and males, a necessary step for a realistic understanding of ornament expression, and contributes to the ongoing discussion on the evolution of elaborate female signal traits.
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ItemInvestigating the loci that contribute to convergent craniofacial evolution between the thylacine and canids( 2018)One of the most fundamental questions in evolutionary developmental biology is how phenotypic adaptations are controlled at the molecular level. One way we can address this question is by looking at examples of convergent evolution between distantly related species. Here we can ask the question; are similarities in morphology reflected by similarities in the genome? One of the most striking cases of convergent evolution in mammals is seen between the marsupial thylacine (or Tasmanian tiger) and placental canids (wolves, dingos and foxes) particularly in their cranial morphology. However, the extent of their morphological convergence has never been directly quantified. In my thesis I use a combination of morphological and molecular data to investigate candidate loci that may contribute to convergent craniofacial evolution between the thylacine and the canids. Using a geometric morphometric comparison of cranial shape between extinct and extant marsupial and placental mammals, I showed that the adult thylacine and canids represent a remarkable case of craniofacial convergence. By additionally CT scanning and landmarking all known thylacine pouch young specimens, I was able to demonstrate that the marsupial thylacine overcame its conserved neonatal constraints towards the end of its developmental period in the pouch. The strong similarities between the thylacine and canids are likely driven by underlying changes in cranial neural crest cells (NCCs), which are directly responsible for patterning the facial skeleton. I next investigated candidate loci that might be underpinning this extraordinary phenotypic convergence. RUNX2 is expressed in NCCs and is strongly implicated in driving facial length evolution in placental mammals. I hypothesized that similarities in the RUNX2 gene might partially explain similarities in facial shape between the thylacine and canids. However, unexpectedly, we found that the marsupials possess an invariant RUNX2 which cannot explain the diversity of facial shapes seen within marsupials nor craniofacial convergence. Instead, changes in facial length might be mediated through regulatory changes to RUNX2 expression. Using a genome-wide approach, we investigated homoplasy in protein coding genes. While overall homoplasy was extremely rare, we identified multiple thylacine/canid homoplasious amino acid substitutions in the osteogenic chromatin remodeller, CHD9, a known upstream regulator of RUNX2. We found that the amino acid substitution in the DNA binding domain resulted in differential expression and activation of RUNX2 in vitro and may act as a contributor to RUNX2-mediated craniofacial convergence. While I found evidence for changes in protein coding genes potentially contributing to convergence, the pleiotropic consequences of mutations in key developmental genes are thought to limit their evolvability. As such, we also used a genome wide approach to investigate accelerated evolution and convergence in the non-coding portion of the genome. We identified multiple putative cis-regulatory elements (CREs), including an enhancer upstream of the craniofacial TGF-β signalling receptor ACVR2A, also critical in NCCs. We found that the thylacine enhancer was able to drive craniofacial expression in the mouse and is a potential candidate mediating convergent craniofacial evolution. This finding suggests CREs may also play important roles in adaptive evolution and convergence. In this thesis I find support for protein coding and CRE evolution driving convergent craniofacial similarities. This supports my hypothesis that convergence targets genes and CREs in the NCCs directing craniofacial convergence between the thylacine and canids.
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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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ItemEvolution of cooperative behaviour in Australian lycaenid butterflies and ants( 2017)Mutualistic associations between butterflies of the family Lycaenidae and ants are common, and the costs and benefits for both partners have been clearly documented. Ant colonies and territories are well defended against intruders of all kinds, thereby providing an ‘enemy-free’ space for the vulnerable caterpillars. In return, tending ants receive a nutritious droplet of food secretions, released by the Dorsal Nectary Organ (DNO). Optimizing ant attendance may be achieved by tailoring the composition and quantity of food rewards to the needs and feeding preferences of the ant colony. Although DNO secretions play a central role in the exchange of benefits within lycaenid-ant mutualisms, cooperation also requires some degree of communication. A critical, unresolved issue in this mutualistic association is how these partners communicate, and in particular how the butterfly larvae are initially accepted by the tending ants. Nestmate recognition in ants is mediated through chemical-based signals, cuticular hydrocarbons (CHCs), and CHC resemblance with the host ant facilitates ant-association across a variety of taxa. Therefore, CHCs are assumed to play a central role in associations of lycaenid butterflies and ants. My thesis research explores the nature of the DNO secretions in three species of the Australian lycaenid genus Jalmenus, J. evagoras, J. icilius and J. ictinus, by investigating the chemical composition of the food rewards and the macronutrient preferences of the workers of ants associated with J. evagoras and J.ictinus. I further investigate how Jalmenus larvae establish ant attendance by examining the CHC composition of J. evagoras larvae and the associated Iridomyrmex mayri ants across a broad and fine geographic scale, and explore the nature and potential resemblance of CHCs between both partners. All three species of Jalmenus provide large quantities of carbohydrates in their DNO secretions, and the tending Iridomyrmex ants show a strong preference for sugar over all single amino acids and amines, except histidine, highlighting a strong concordance between the abundance of different macronutrients synthesised by lycaenid butterfly larvae and the preference of their attendant ants. However, Iridomyrmex ants prefer amino acids other than the most abundant in the larval DNO secretions, suggesting that the larvae may optimise the costs and benefits of amino acid production. Remarkably, lycaenid DNO secretions contain an astonishing number of compounds, some of which may be key nutrients and thus play a significant role in lycaenid-ant associations. This thesis reveals significant and unexpected compositional differences of CHCs between I. mayri colonies. Remarkably, host tree-specific CHC profiles are also found in the associated butterfly J. evagoras. Although resemblance of the overall CHC composition between the two partners was not detected, the great variation of CHC profiles suggests that CHCs serve a function other than purely physiological, possibly as communication signals. This is supported by my findings that workers of I. mayri react significantly less aggressively towards the extracts of larvae that had been tended by nestmate workers compared with larvae that had been tended by non-nestmates. These data are consistent with the variation in cuticular compounds: ants and larvae from the same host tree generally share a number of cuticular compounds that distinguish them from that of other trees. However, host colony-specific compounds may be acquired by J. evagoras larvae through contact with the I. mayri colony. My field experiments show that ant attendance clearly modifies the cuticular blend of J. evagoras larvae, but this was not the simple addition of ‘new’ compounds. When presented with a living early instar larvae, unlike extracts, the frequency of ant aggression was negligible, suggesting that workers of I. mayri use cues other than or in addition to cuticular compounds to recognise lycaenid caterpillars as mutualistic partners. Overall, the findings of this thesis offer new insights into the evolution of cooperative behaviour in lycaenid-ant associations, and provide a valuable addition to the current state of knowledge on chemically-mediated signalling in a mutualistic system.
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ItemAlternative splicing and stage differentiation in apicomplexan parasites( 2017)Alternative splicing is the phenomenon by which single genes code for multiple mRNA isoforms. This is common in metazoans, with alternative splicing observed in over 90% of human genes (Wang et al., 2008). However, the full extent of alternative splicing in apicomplexans has been previously under-reported. Here, I address this deficiency by transcriptomic analysis of two apicomplexan parasites: Toxoplasma gondii, which causes toxoplasmosis; and Plasmodium berghei, which is a murine model for human malaria. I identified apicomplexan homologues to SR (serine-arginine–rich) proteins, which are alternative-splicing factors in humans. I then localised a homologue, which I named TgSR3, to a subnuclear compartment in T. gondii. Conditional overexpression of TgSR3 was deleterious to growth. I detected perturbation of alternative splicing by qRT-PCR. Parasites were sequenced with RNA-seq, and 2000 genes were identified as constitutively alternatively spliced. Overexpression of TgSR3 perturbed alternative splicing in over 1000 genes. Previously, computational tools were poorly suited to compacted parasite genomes, making these analyses difficult. I alleviated this by writing a program, GeneGuillotine, which deconvolutes RNA-seq reads mapped to these genomes. I wrote another program, JunctionJuror, which estimates the amount of constitutive alternative splicing in single samples. Most alternative splicing in humans is tissue specific (Wang et al., 2008; Pan et al., 2008). However, unicellular parasites including Apicomplexa lack tissue. Nevertheless, I have shown that alternative splicing can still be common. I hypothesised that the tissue-specific alternative splicing of metazoans is analogous to stage-specific alternative splicing in unicellular organisms. I purified female and male gametocytes of P. berghei and sequenced these stages, with the aim of investigating alternative splicing and its relationship to stage differentiation. As a reference point, I first established the wild-type differences between female and male gametocytes. I detected a trend towards downregulation of transcripts in gametocytes compared to asexual erythrocytic stages, with this phenomenon more marked in female gametocytes. I was also able to identify many female- and male-specific genes, some previously-characterised, and some novel. My findings were further placed in an evolutionary context. Sex-specific genes were well conserved within the Plasmodium genus, but relatively poorly conserved outside this clade, suggesting that many Plasmodium sex-related genes evolved within this genus. This trend is least pronounced in male-specific genes, which suggests that sexual development of male gametocytes may have preferentially evolved from genes already present in organisms outside this genus. I then analysed these transcriptomes, now focusing on changes in alternative splicing. While non-gendered gametocyte differentiation is modulated by known transcription factors such as AP2-G (Sinha et al., 2014), I provide evidence that alternative splicing adds another level of regulation, which is required for differentiation into specific genders. I ablated a Plasmodium SR-protein homologue, which I named PbSR-MG. By transcriptomic analysis, I show that it regulates alternative splicing, predominantly in male gametocytes. Ablation was also associated with a drastic reduction in the viability of male gametocytes. Hence, I have shown that alternative splicing is common in apicomplexan parasites, is regulated by specific genes, and acts on specific targets. Alternative splicing is important for parasite viability and fundamental to stage differentiation in Plasmodium.
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ItemResolving the evolutionary history of the Australian grass trees, Xanthorrhoea (Xanthorrhoeaceae), using multiple high-throughput sequencing techniques( 2016)Xanthorrhoea (Xanthorrhoeaceae subfamily Xanthorrhoeoideae) is an iconic component of the Australian flora, occurring in heathlands, woodlands and dry sclerophyll forests in eastern and south-western Australia. The last revision of the genus in 1986 recognised 28 species and five segregate subspecies. However, Xanthorrhoea taxonomy can be challenging due to limited variation in vegetative morphology; identification relies primarily on continuous characters which vary within and between species. Geographical information is often heavily relied upon for identifications, yet some species have overlapping distributions. A comprehensive molecular phylogeny incorporating all currently described species and infraspecific variants is required to understand relationships between species, biogeographical patterns, and to resolve taxonomic issues in Xanthorrhoea. High throughput sequencing is significantly changing the way plant systematics research is done; the sheer volume of genetic data obtainable at a low cost per base pair allows for greater sample numbers and more thorough investigation of evolutionary relationships. In this thesis, I use multiple high-throughput sequencing methods to generate nuclear and plastid datasets for resolving evolutionary relationships in Xanthorrhoea. Targeted amplicon sequencing was performed on over 150 samples of Xanthorrhoea for eight plastid loci, forming a detailed phylogeographic investigation of a widespread genus across the Australian mesic zone. Three distinct haplotype groups were identified: one mostly in Western Australia; one in south eastern Australia; and one in north eastern Australia. The divergence between eastern and western populations is suggested to be caused by vicariance events associated with the formation of the arid zone. The approximate geographic location of the genetic border between north eastern and south eastern Australian haplotype groups is near the Southern Transition Zone in eastern New South Wales, which has been identified as a region of genetic distinction in several plant and animal lineages. Several Queensland samples had haplotype sequence related to Western Australian samples, which is likely caused by failure of widespread ancestral plastid variation to coalesce within a species or geographical region. Targeted amplicon sequencing of four low copy nuclear genes displayed the feasibility of this method for separating allelic variants in heterozygous samples. Phylogenies based on alignments of the individual phased loci (i.e., including all allelic variants for an individual) indicated incomplete lineage sorting, with allelic variation within species, widespread sharing of alleles between species, and a lack of geographic structure. However, phylogenetic analysis methods that utilised both the allelic variation within a locus and combined data from all four loci resolved phylogenies showing some taxonomic and geographic structure. Analysis of unphased loci (i.e., alleles within an individual not distinguished) showed a complete lack of resolution, with most of the species resolved as a polytomy. While a fully resolved phylogeny of Xanthorrhoea was not obtained, results from this study show the value of considering the allelic variation of nuclear loci, and indicate that incomplete lineage sorting is a major factor affecting accurate resolution of a phylogeny for the genus. Restriction associated DNA sequencing, (RADseq) is a powerful method for obtaining thousands of loci from throughout the genome of an organism. A modified double-digest RADseq method was used to explore relationships among the Western Australian species. Three clades of WA taxa were identified, and relationships between taxa were well-resolved, except for X. preissii and X. brunonis; these two species together formed a well-supported clade, but genetic variation within the clade did not correlate with current species limits as defined by morphological characters. Scanning electron microscope images of leaf micromorphology indicated some morphological variation useful to distinguish clades and some species. The phrase name entity X. sp. Lesueur was supported as a distinct genetic lineage worthy of recognition, and will be published as Xanthorrhoea lateritica1. A PCR based reduced representation library method, using random primer sequence to amplify multiple loci from the genome was developed to resolve the phylogeny of Xanthorrhoea. Over 3000 loci were sequenced and used to resolve the phylogeny of Xanthorrhoea. Rogue samples that occupy multiple positions within a set of bootstrap trees caused a significant reduction in phylogenetic resolution. Removing rogue samples increased phylogenetic resolution, identified seven clades of taxa, and clarified relationships among species. Rogue samples were not related to sequencing or locus filtering issues, and may be due to incomplete lineage sorting or hybridisation. Three clades of eastern Australian species were identified; these clades were supported by leaf surface micromorphology and geography. In all datasets, determining genetic relationships between species or geographical regions was difficult in Xanthorrhoea: this is attributed to evolutionary factors such as incomplete lineage sorting and hybridisation, or low sequence variation, as opposed to methodological issues. Explanations for the effect of these factors in Xanthorrhoea were related to life history traits, including a long generation time, fire stimulated flowering, large population sizes, and recent speciation events associated with environmental changes during the Quaternary. Several taxonomic issues arising from the results of this research are discussed, including taxa requiring new circumscriptions or reappraisal.
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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.