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.