No description available.

No description available.

No description available.

For many species, vision contributes to a number of fitness-related tasks, including mating and the detection of prey and predators. Selection on the visual system should therefore be strong, especially when ecological or genomic changes open new avenues for evolutionary changes. Visual system proteins are thus attractive systems for molecular evolutionary analyses. This thesis presents a collection of evolutionary studies on two gene families, opsins and crystallins. Opsin proteins determine the wavelengths of light detected by the retina, while crystallin proteins contribute to lens transparency and refractory power. My studies focus on teleost fishes, because teleost visual ecology is exceptionally diverse and because gene duplication is common in this group. In Chapter One, I outline the relevance of protein variation to organismal evolution and describe the analytical methods employed throughout this thesis. Chapter Two considers the long-wavelength sensitive (LWS) opsins of the guppy (Poecilia reticulata). The guppy is shown to possess multiple LWS opsins that have accumulated differences at functionally important amino acid sites since duplicating. Chapter Three focuses on the guppy’s main predator, the pike cichlid Crenicichla frenata, which is shown to have a greater capacity for short-wavelength vision than previously believed. However, this cichlid possesses three fewer opsins than closely-related African cichlids, a difference partly due to duplication of a green-sensitive (RH2) opsin in African cichlids. In Chapter Four, this RH2 duplication event is studied in greater depth; variation in selective constraint is documented following gene duplication and between species from different lakes. Some of the analytical methods employed in Chapter Four were newly developed, as detailed in Chapter Five, where a test for functional divergence among clades is evaluated and then improved upon through the presentation of a new null model that better accommodates among-site variation in selection. In Chapter Six, phylogenetic relationships within the βγ lens crystallin superfamily are clarified, and the functionally distinct γN family is shown to have evolved conservatively compared to other crystallin families. The thesis concludes with suggestions for future directions for evolutionary research on opsins and crystallins, and summarizes recent work that has built on these studies.

The dissertation examines one of the most remarkable and controversial developments in the recent history of European integration, namely the institutionalization of a regional policy regime to manage the continent’s frontiers. By adopting this regime (known in policy circles as ‘Schengen’), European governments have in fact relinquished part of their sovereign authority over the politically sensitive issue of border control, thereby challenging what for a long time was the dominant national approach to policy-making in this domain. In order to account for the regime’s emergence and success, a constructivist analytical framework centred on the notion of ‘cultures of border control’ is advanced. From this perspective, the adoption of a regional approach to govern Europe’s frontiers is the result of the evolution of a nationalist (‘Westphalian’) culture—or set of background assumptions and related practices about borders shared by a given policy community—into a post-nationalist one (‘Schengen’). The cultural evolutionary argument elaborated in the dissertation captures the unique political dynamics that have characterized border control in Europe in the last two decades and offers a more nuanced account of recent developments than those available in the existing European Studies literature. It can also shed light on current trends defining European politics beyond border control (e.g., Europe’s policy towards its neighbours) and on other attempts to regionalize border control outside Europe (e.g., the proposal for a North American security perimeter).

Multicasting in Long-Term Evolution (LTE) environments poses several challenges if it is to be reliably implemented. Neither retransmission schemes nor Forward Error Correction (FEC), the traditional error correction approaches, can be readily applied to this system of communication if bandwidth and resources are to be used efficiently. A large number of network parameters and topology variables can influence the cost of telecommunication in such a system. These need to be considered when selecting an appropriate error correction technique for a certain LTE multicast deployment. This dissertation develops a cost model to investigate the costs associated with over-the-air LTE multicasting when different error correction techniques are applied. The benefit of this simplified model is an easily implementable and fast method to evaluate the communications costs of different LTE multicast deployments with the application of error correction techniques. / MIng (Computer and Electronic Engineering), North-West University, Potchefstroom Campus, 2014

In a population of altruists, all individuals thrive. But altruists are exploited by cheating individuals which do not perform altruistic acts but still benefit from those. In these conditions cooperation cannot easily evolve. This issue is resolved by kin recognition: altruists recognise each other through the use of a conspicuous tag. These altruists do well until cheaters acquire the signalling tag and disrupt the cooperation. But altruists using a different tag can then invade the population, followed by new cheaters. This mechanism can lead to a diversity of tags coexisting in the population. However it has not yet been applied in realistic biological systems. In this thesis, I formulated mathematical and simulation models to investigate the effect of diversity on the evolutionary dynamics in systems where different altruists compete with cheaters. In particular, I focused on organisms producing public goods, i.e. goods that can profit to the whole population. I considered two biological systems models: gynodioecious populations of plants, where hermaphrodites produce pollen that can be used by female-only individuals, and bacteria producing an iron-chelating molecule, called siderophore, that can be exploited by both producers and non-producers. I found that diversity in gynodioecious plants is dependent on population structure. In particular, I found that the maximal level of diversity occurs when the population structure does not favour altruists or cheaters. Next, I found a number of important results in siderophore-producing bacteria. By considering a detailed ecological model, I derived Hamilton's rule in a metapopulation and found that the level of cooperation in a population depends on the length of interaction between strains. Finally, I discovered a novel evolutionary mechanism generating and maintaining diversity and showed that it results from non-equilibrium mechanisms. These findings explain why cheaters appear readily in experiments but are rare in natural populations. My results demonstrate the importance of integrating ecological details in order to understand the mechanisms leading to cooperation and diversity, and will provide a basis and framework for future studies on the emergence and maintenance of diversity.

Genetic variation contains detailed and quantitative evidence about the history of populations. The historical traces of demographic growth and contraction, as well as the history of human disease, have left traces on the patterns of modern variation and can be studied by sampling present-day populations. However, the data sets that are necessary in order to take full advantage of this living archaeological record have not been available until recently. The quality and quantity of data have increased dramatically during the past decade because of the identification of polymorphisms, including SNPs and microsatellites, that are much more amenable to mathematical modeling and efficient genotyping than earlier marker systems. The research in this thesis has been carried out in response to the need to provide new methods of analysis to match the new types of data. Chapter 1 describes multilocus tests of demographic history and their application to real data. Chapter 2 describes how the pattern of linkage disequilibrium around a disease-predisposing mutation can be used to estimate the date of a mutation that is, the age of the most recent common ancestor of a set of modern samples. Finally, Chapter 3 draws several direct connections between human evolutionary history and medical genetics.

This study aims to determine the late-Quaternary evolution of an ephemeral, transverse river system developed in southeast Spain, with particular reference to sediment provenance variation. The Rio Alias drains two inter-montane east-west orientated Neogene sedimentary basins; the Sorbas and Almeria basins. Pliocene to present transpressional tectonics has led to inversion of the sedimentary basins and incision of the developing fluvial system. Fluvial incision has led to the preservation of a suite of alluvial terraces recording the late-Quaternary development of the Rio Alias. Fluvial system inauguration began in the Plio-Pleistocene epoch. The primary fluvial system developed as a consequent river later becoming superimposed and transverse to structure. The drainage basin of the Rio Alias has been sub-divided into 4 sub-basins; The Lucainena, Polopos, Argamason and El Saltador sub-basins. Each basin is structurally controlled. The impact of climate, tectonics, river-capture and eustatic sea-level variation on the fluvial system evolution varies both spatially and temporally across the sub-basins of the Rio Alias. Across the region alluvial aggradation is thought to relate to global glacial periods and incision to interglacial periods. The Lucainena sub-basin is largely controlled by climatic variation related to glacial interglacial cycles with slight modification due to local small scale river-capture and regional epeirogenic uplift. The Polopos sub-basin is also largely controlled by climatic variation, however a major river-capture event c.70ka beheaded the Rio Alias of c.70% of its drainage area. Following the loss of drainage the beheaded Rio Alias system lost stream power, this is reflected in the decrease in size of bedform geometry and the reduced incisional capacity of the fluvial system of the post-capture terrace sequence. In the Argamason sub-basin the Rio Alias crosses the Carboneras Fault Zone, a left-lateral strike slip fault. Late-Quaternary tectonic activity has significantly modified the climatically generated signal. Large tortuous meanders developed in response to normal tectonic activity and continued tectonically driven base-level lowering led to abandonment of terraces and local incision. The El Saltador sub-basin is located at the seaward end of the system and the climate generated phases of aggradation and incision have been greatly complicated by eustatic sea-level variation related to glacial/interglacial cycles. The lowering of base-level due to sea-level regression initially led to pronounced incision along steep gradients and to the development of meander loops in the seaward end of the Rio Alias, during what regionally was a climate driven phase of aggradation. Analysis of the alluvial sediment using a combination of field based clast analysis and laboratory analysis (petrology, SEM, magnetic analysis) allows a detailed picture of sediment provenance variation to be established throughout the evolution of the Rio Alias. Provenance analysis provides information on the timing and extent of river-capture related loss of drainage area, the relative timing of local tectonic activity and also provides new information regarding sediment source area variation throughout the development of the fluvial system. Detailed analysis of the terrace sediments and the modern channel indicates that as the fluvial system incises, local input of sediment from the steepening valley sides grows increasingly dominant. The coupling between the hillslopes and the channel thus changes through time. Sediment provenance analysis has increased our understanding of the long-term fluvial evolution of the Rio Alias, identifying not only sediment provenance variation due to river-capture and changing geology but to fluvial system development.

In recent decades we have learned that cooperation is an important and pervasive feature of microbial life. This revelation raises exciting possibilities. On the one hand, we can now augment our understanding of how social phenomena evolve by using microbial model systems to test our theories. On the other hand, we can use concepts from social evolution to gain insight into the biology of the microbes we hope to control or kill. In this thesis I explore both possibilities. First, I consider the theoretical problem of how and when microbial cooperation might be subject to frequency- and densitydependence. Formerly, vague theory and a scant, sometimes contradictory empirical literature made it unclear when such patterns could be expected. Here, I develop theory tailored to a microbial context, and in each case, I test key predictions from the theory in laboratory experiments, using as my model trait the production of siderophores by the bacterium Pseudomonas aeruginosa. Secondly, I consider the ecological consequences of cooperator-cheat dynamics in the context of an infection. Specifically, I use experimental infections of diverse host models to investigate the role of two cooperative traits, siderophore production and quorum sensing, in the pathogenesis of P. aeruginosa. When a successful infection requires cooperation among pathogens, theory predicts that conflict among coinfecting strains can undermine cooperation and hence decrease virulence; whereas, in the absence of cooperation, conflict could lead to heightened exploitation and hence increased virulence. This exciting idea has received little empirical attention to date but here I address this using multiple pathogen strains, multiple social traits, and multiple model hosts.