The ecology and evolution of pathogens are key factors in predicting the severity and spread of disease, as well as treatment outcomes. However, the effects of multiple trophic levels that include host, microbial competitors and viruses are typically overlooked. In this thesis I develop our understanding of bacteria-phage coevolution, microbial dispersal and the role of the microbiome in disease. The results of these experiments have direct implications for phage therapy: the use of bacteriophages to treat bacterial infections. Firstly, I explore the risks of phage application in the environment and draw parallels with the misuse of antibiotics in selecting for bacterial resistance. I then demonstrate that the evolution of resistance to phages in a plant pathogenic bacterium is context-dependent. Notably, I find a fitness cost in plant infections that is absent when the bacteria are cultured solely in the laboratory. I then characterize four novel phages and use a simple laboratory based assay to predict their potential as phage therapy agents in an agricultural context. Next I show that reservoir species of plant hosts can affect the evolution of virulence, when bacteria are passaged on both a focal and distant host, but find no evidence of local adaptation. I also show that the evolution of such traits can occur in a parallel manner at the genetic level. I then determine a compositional shift in the microbiota associated with the symptoms of bleeding canker disease in Horse Chestnut trees across the length of the UK. Finally, I find an age-elated decline in bacterial species richness and evidence for niche-assembly theories by investigating bacterial dispersal in UK Oak trees in a single woodland.

<p> Biological sex estimation has been a central tenant in physical anthropology and bioarchaeology since the foundation of the fields. Traditionally, sex estimation techniques have centered on pelvic morphology but features of the pelvis are often poorly preserved in forensic and archaeological contexts. However, teeth have very high preservation potential. Because the crown is susceptible to ante- and postmortem damage, the cementoenamel junction (CEJ) provides a more often preserved portion of the tooth. Several studies have shown the potential use of measurements of the CEJ in biological sex estimation; however, these studies have been limited in their scope, samples sizes, and materials utilized. Additionally, the role of biological affinity in the estimation of biological sex from measurements of the CEJ have not been fully explored. Three main goals of the present study are: 1) to assess the ability to estimate biological sex from measurements of the cementoenamel junction across populations; 2) to assess the role of biological affinity in sex estimation based on the measurements of the cementoenamel junction across populations; and 3) to examine the relationship between dental arcade size and biological sex within and between populations. </p><p> A total of 737 dentitions (7,369 teeth) from American and South African Whites and Blacks were measured based on buccal-lingual and mesial-distal CEJ measurements defined by Hillson and colleagues (2005). Percent dimorphism was calculated for buccal-lingual, mesial-distal and geometric mean measurements for each tooth. Percent dimorphism was highest in the canines for all groups. Discriminant function and logistic regression analyses were run to assess the ability of the measurements to correctly classify biological sex within and between populations and groups. Correct classification ranged from 84.1% to 90.7%. Within group comparisons (i.e., American females, South African males, etc.) highlighted that molars, premolars, and incisors have the greatest weight in the discriminant function in classifying differences between ancestral groups.</p><p> Finally, a total of 162 dental arcades (maxillary and mandibular) were measured from photographs using <i>ImageJ</i> software to assess differences in dental arcade size and to assess the relationship between mesial-distal measurements of the CEJ and the length of the dental arcade. Statistically significant differences in mean arcade size were found for all groups except South African Whites and South African Blacks (mandible only). Pearson&rsquo;s correlation coefficient tests were used to test if a correlation existed between the sum of the mesial-distal CEJ measurements and the total arc length. A significant correlation was found in all groups except American Whites, South African Whites, and All Whites combined (mandible only). In summary, the buccal-lingual and mesial-distal measurements of the CEJ can be used to estimate biological sex with a high degree of correct classification. Canines, specifically the lower canine, shows the highest percent of sexual size dimorphism for all groups. Lower overall sexual size dimorphism is noted in the South African groups, especially South African Whites, when compared with their American contemporaries. Results indicate that the size (and possibly the shape) of molars, premolars and incisors have the most influence on differences seen between ancestral groups.</p><p>

Ph.D. (Education) / This research focused on two short learning programmes in evolution education offered by the Department of Science and Technology Education in the Faculty of Education of the University of Johannesburg. The broad purpose of the study was to develop design principles for a series of short learning programmes on evolution offered by the University. In achieving these aims, the study looked at teachers’ conceptual understanding of evolution, which included a number of common myths and misconceptions; folk or naive evolutionary explanations; and affective and sociocultural factors that influence cognition. Results were obtained from questionnaires, narratives, observations, discussion, and pre-and post-tests. A fruitful analytic tool was developed – that of converting questionnaire responses into narratives in order to obtain a better within participant view of coherent versus fragmented thinking. Some the themes that emerged included the cognitive bias of essentialism and how this relates to the notion of phenomenological primitives or p-prims, and the mechanism of resubsumption. "Hot" and "cold" learning and the critical issues of both religious and racial objections to evolution emerged as a fairly dominant theme. Data also supported a view of knowledge-as-pieces rather than theory-like in this knowledge domain. Poor teacher knowledge and the need for longer learning programmes, are also discussed in the results. To mitigate these conceptual and affective barriers, a number of design principles are proposed and discussed for teacher professional development in this area including the importance of communities of practice to augment short learning programmes and support on-going professional development.

No description available.

The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.

Copper-containing nitrite reductase (NiR) is a homotrimer of two cupredoxin domains and catalyzes the single electron reduction of NO2- to NO during dissimilatory denitrification. To investigate the evolution of NiR, methods of mutagenic library generation and high-throughput variant screening from E. coli colonies were developed. These methods allow for facile screening of 105 mutants for folding efficiency or substrate specificity. Initial proof of principle studies yielded several variants that oxidized the artificial substrate ο-dianisidine up to 8 times faster than wild type NiR, suggesting that this methodology has the potential to engineer NiR to acquire other reductase functions. A crystal structure was solved for a putative multicopper oxidase (MCO) and NiR homologue from Arthrobacter sp. (AMMCO) to 1.8 Å resolution. The overall folds of AMMCO and NiR are very similar (r.m.s.d. of 2.0 Å over 250 Cα atoms); Like NiR, AMMCO is a trimer with type-1 Cu sites in the N-terminal domain of each monomer; however, the active site of AMMCO contains trinuclear Cu site characteristic of MCOs instead of a the mononuclear type-2 Cu site found in NiR. Detailed structural analysis supports the theory that two-domain MCOs similar to AMMCO were intermediaries in the evolution of NiR and the more common three-domain MCOs. The physiological function of AMMCO remains uncertain, but genomic, crystallographic and functional analysis suggests that the enzyme is involved in metal regulation. Considering the extensive similarity between AMMCO and NiR, particularly at the active site, engineering a trinuclear cluster into NiR appears feasible with a modest number of alterations to the polypeptide chain. With the aid of my newly developed high-throughput screening technique and site-directed mutagenesis, the mononuclear NiR active site was remodelled into a trinuclear Cu site similar to that of MCO. A crystal structure of this variant was solved to 2.0 Å and the presence of three copper atoms at the engineered cluster was confirmed by Cu-edge anomalous diffraction data. Although the trinuclear copper cluster is present and catalyzes the reduction of oxygen, achieving rates of catalysis seen in native MCOs has proven more difficult. With the framework provided, further engineering NiR into a robust MCO is likely to provide further insights into the structural basis of oxygen reduction by trinuclear copper sites. / Medicine, Faculty of / Biochemistry and Molecular Biology, Department of / Graduate

Much scientific and media attention has been devoted to the growing body of research into the genetic correlates of human phenomena. However, many of the resulting reports lead to a deterministic interpretation of the role of genes, and involve fundamental misunderstandings of genetics and heredity. Hence, questions arise regarding the ways in which people make sense of the behavioural genetics research they encounter in everyday life. Furthermore, essentialist accounts are often embedded within popular understanding of politically sensitive topics, such as eugenics, race, and sex, and therefore it is important to examine how people comprehend genetic influences on behaviour. In this dissertation, I review current findings regarding the effects of genetic attributions on beliefs, attitudes, and behaviours in the context of the social world. Particular attention is paid to such effects in the context of gender issues. Specifically, in three studies I examine the effects of exposure to scientific theories concerning human sexuality on attitudes towards and evaluations of men’s dubious sexual behaviors. The results indicate that among men exposure to evolutionary psychology arguments leads to more lenient evaluations and judgments of an array of dubious sexual behaviors, compared with exposure to social constructivist arguments. It also seems that men implicitly hold nativist perceptions with regards to male sexuality and promiscuity. The findings were less conclusive among women, with some indication that women are less affected by such exposure as well as less likely to naturally hold a nativist perspective in the context of human sexuality. This empirical research has direct implications for previously suggested intervention programs and adds to the incurrent resurgence of interest in the effects of genetic theories. Finally, I identify areas where further exploration is needed, suggest potential solutions for specific problems, and evaluate related individual and social implications. / Arts, Faculty of / Psychology, Department of / Graduate

In recent years, microRNAs (miRNAs) have been recognised as important genetic regulators of gene expression in Animals and Plants. They can potentially target a large fraction of the cellular transcriptome, having been shown to be important for diverse biological processes such as development, cell differentiation, proliferation and metabolism. The publication of the Human genome in 2001 marked the start of a great community effort to sequence a variety of other species. These data have great potential for comparative genomics, that can lead to better biological understanding. Some miRNA families are known to be highly conserved, across long evolutionary distances, many found in co-transcribed clusters across the genome. While these phenomena have been previously reported, a large-scale analysis of evolutionary patterns was still lacking. Furthermore, the rate at which new relevant data is being made available makes it challenging to keep up and many of the evolutionary studies performed before are now significantly out of date. This thesis describes a number of approaches taken to analyse miRNA datasets, harnessing the full potential of currently available data for comparative genomics. These were used, not only to revisit many of the notions in the field with a larger and updated dataset, but also to develop novel strategies that enable a coherent view of miRNA evolution at different evolutionary time-scales. A new tool, described within this thesis, was developed for large-scale, species independent miRNA mapping. An assessment of the evolution of the miRNA reper- toire across species was performed, together with detailed sequence conservation analysis and miRNA family clustering. Phylogenetic profile analysis uncovered in- teresting co-evolution between miRNAs and protein coding genes. The genomic organisation of miRNAs and their conservation across species was also studied, pro- viding detailed conserved synteny maps for miRNAs and proteins across more than 80 species. Finally, at the intra-specific level, I analysed the occurrence of single nucleotide polymorphisms affecting miRNA loci or their predicted target sites. All the tools built and integrated in this research were made available to the community and designed to be easily updated, making it easier to keep up with the data that is constantly being made available. Many aspects of miRNA biology are still being uncovered, and the ability to easily put these findings into an evolutionary context will potentially be useful for the community.

The fossil record is the only direct source of data for studying modes (patterns) and rates of morphological change over geologic time periods. Determining modes is critical for understanding macroevolutionary processes, but just how modes can vary within a taxon, and why, have hitherto been largely understudied. To address this, I examined patterns of morphological change in the shell of the Mesozoic marine bivalve genus Buchia over its geographic and temporal range. Buchia was chosen as a test subject because it is abundant, well-preserved across a variety of facies, and is widely distributed across the Northern Hemisphere where the likelihood of multiple lineages is low. While the focus of this thesis is on evolutionary patterns, it is also necessary to address issues of taxonomy and geographical variation, making this research applicable to a wide-variety of fields. Previous to this study there was no protocol for measuring buchiid valves, nor was the genus studied in a quantitative manner. Throughout this research I used ten morphological characters to describe shell shape and size. Multivariate methods (principle component and canonical variate analyses) were employed to discriminate between species of Buchia and examine how morphological characters change through time and space within the genus. Evolutionary patterns were delineated using two well-established programs that discriminate between multiple modes of evolution. Overall, nearly 2000 specimens from eight geographical locations around the world were studied for this thesis. I found the genus Buchia was a useful tool for evolutionary studies as it can be studied quantitatively in space and time. Specically I have found that buchiid species can be delineated using morphometrics; the genus is restricted to the Northern Hemisphere; while the environment significantly affects morphology, there is no evidence of a latitudinal gradient; diversity and disparity within Buchia are not correlated; most evolutionary modes conformed to random walks or stasis; and modes and rates vary across the geographical range of the genus. Overall, I have found that the environment plays an important role in shaping both morphology and modes. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

In this thesis we investigate the evolution of galaxies since z = 3. There are several methods to measure the star formation rate (SFR) of galaxies, they all however have drawbacks. Several studies have investigated the SFR at high redshifts using SFR trac­ers that suffer from uncertainties, either from the tracer used, or from the uncertainties correcting for the effects of dust. We have new measurements of the Ha emission line for a sample of galaxies at =~1; Ha is a more accurate SFR-tracer than other com­monly used tracers, but until now had been technically difficult to measure at : > 0.85. We investigate methods to correct these observations for dust and we use these mea­surements to investigate the relation between SFR, stellar mass and colour. We find that there is a drop in the fraction of massive (M, > 1011 M.) star-forming galaxies at = < 0.9 and that the fraction of all galaxies that are star-forming drops steadily and significantly with redder (U — B) colours. We find that the M„-SFR (galaxy main sequence, GMS) is flatter than previously measured and that for the most massive galaxies, star formation shuts off abruptly at =~1.