No description available.

No description available.

The cycle of star formation is the key to galaxy evolution. Stars form in massive collections of extremely dense cold gas. Stellar feedback will inject turbulence into the interstellar medium (ISM) and regulate the availability of more star-forming gas. This gas is an integral component in the cycle of star formation but is very difficult to model in numerical simulations. We have investigated the interplay between star formation and the structure of the ISM in numerical simulations. These simulations were done using the Smoothed Particle Hydrodynamics code Gasoline. For this work we introduce a new treatment for photoelectric heating in Gasoline. We first explore the impact of numerical parameter choices for the star formation threshold density, star formation efficiency and feedback efficiency. Of these three parameters, only the feedback efficiency plays a large role in determining the global star formation rate of the galaxy. Further, we explore the truncation of star formation in the outer regions of galactic discs and its relation to the presence of a two-phase thermal instability. In the outer regions of the simulated discs, gas exists almost exclusively in one warm phase, unsuitable to host large-scale star formation. We find that the disappearance of two-phase structure in the ISM corresponds to the truncation of star formation. / Thesis / Master of Science (MSc)

Wing shape and echolocation are two novel adaptations in the Chiroptera and are strongly influenced by environmental conditions. Wing shape is influenced by environmental clutter. Shorter, broader wings allow for more maneuverable flight, and are advantageous for bats living in highly cluttered environments. Longer, narrower wings help bats to increase flight speed, and are best suited for bats living in more open environments. It is likely that wing shape is also influenced by temperature, given the potential for wings to act as thermoregulatory appendages. Wings provide a thermal gradient across their surfaces, dissipating excess heat from the body. However, the importance in thermoregulation in determining wing size is unknown. If thermoregulation is a strong selective pressure, bats in hotter, more arid regions should have larger wings. Environmental conditions also influence echolocation pulse design. Echolocation pulses must successfully reach a target and generate an audible echo despite atmospheric attenuation. High-duty cycle (HDC) pulses, calls with longer durations than the interval between them, are particularly useful in environments with high amount of environmental clutter. HDC echolocators use an acoustic fovea and Doppler shift compensation to detect the fluttering wings of insect prey in dense vegetation. However, the flexibility of these pulses is limited by the bat's acoustic fovea. Wing shape and echolocation combined form an adaptive complex, providing bats with a highly specialized system of foraging. Climate change poses an enormous risk to a bat's foraging success, because rising ambient temperatures are likely to change the selective pressures on wing size (due to the potential thermoregulatory benefits) as well as prey detection volumes of the bat's echolocation (because sound propagation is influenced by temperature). As an adaptive complex any selection on either wings or echolocation is likely to influence changes in the other, with consequences for the foraging efficiency of bats. The potential impact of climate change on the foraging efficiency of bats can be gauged by the bats' adaptive responses to different climatic conditions over their geographic range. I examined these two traits in different localities across the geographic range of the Cape horseshoe bat, R. capensis to determine if wing and echolocation parameters are adapted to current climatic conditions. I measured wing area and echolocation parameters at sites within the distribution of R. capensis that were representative of the different climates across its range. I measured wing areas using digital image analysis software, and I measured echolocation parameters using a microphone array system. Temperature was a predictor in the top fitting linear mixed effects models for both wing area and prey detection volume. For differences in wing area, body mass was the only significant explanatory variable. However, body mass may itself be influenced by environmental conditions. NDVI, latitude, and average winter minimum temperature significantly related to differences in prey detection volume. My results indicate geographic variation in both wing area and prey detection volume, an indication that these traits are adapted to local climate conditions. Geographic variation in wing area is a consequence of body mass, which may or may not be a function of climate. However, geographic variation in prey detection volume is directly influenced by the environment. Therefore, increases in ambient temperature due to human-induced climate change are likely to have an effect on the foraging efficiency of R. capensis.

Our understanding of speciation has been greatly improved with advances in genomic technology, but most of our knowledge of speciation is still built on research of diploid systems. Polyploids, however, are found in many lineages across the tree of life and exhibit considerably different evolutionary dynamics than diploids. Here, we investigate patterns of population structure and divergence in a system of two allopolyploid species of Mimulus (monkeyflower) that occur sympatrically in Chile: M. luteus and M. cupreus. We find that while the two species have consistent phenotypic differences across the range, they are genetically clustered into a northern and southern population (rather than by species), based on a STRUCTURE analysis of 48 whole-genome paired-end sequences of the two species across six populations in Chile. Using LUMPY and DELLY2 to locate chromosomal structural variants (SVs), we identify hundreds of SVs unique to one species or the other both across the entire range and just within the north or south. We also calculated metrics of divergence (FST and DXY) in 10 kbp regions across the genome and find that these metrics were not greater within SV regions than across the whole genome. However, we did find that inversions occurred at 100–150X greater frequency within the regions of top 1% of FST and DXY values compared to the across the entire genome, indicating that inversions may promote divergence. Overall, we find evidence to suggest that M. luteus and M. cupreus are currently undergoing sympatric speciation, and that inversions may help promote divergence in this system while deletions and duplications likely do not. Additionally, SV diversity is much higher than generally assumed, perhaps due to increased genomic instability in these allopolyploids, warranting future studies looking into the effects of SVs on species divergence.

The ribbonfish family Trachipteridae (Lampridiformes) includes three well-defined genera (Trachipterus, Desmodema, and Zu), which are distributed worldwide throughout the pelagic marine environment as with most families of Lampridiformes, drastic changes in morphology occur throughout ontogeny due to extreme allometric growth. Combined with the rarity of specimens, this has led to the description of different life history stages as different species, rather than as part of the ontogenetic continuum of a single species. There is significant uncertainty concerning the ontogeny, distribution, nomenclature, number and phylogenetic affinity of trachipterid and other lampridiform genera.;The first chapter of my dissertation is a taxonomic review of of the family Trachipteridae. This chapter provides updated genus (Trachipterus, Desmodema, and Zu) and species descriptions ( Desmodema and Zu) and a synthesis of life history, biogeographic, and ontogenetic data for trachipterid fishes, including examination of an abundance of material from the western Pacific Ocean. Additionally, numerous new morphological observations are described and an updated key to the trachipterid genera, applicable to both juvenile and adult stages, is provided.;The phylogenetic systematics of all lampridiform genera (Metavelifer, Velifer, Lampris, Lophotus, Eumecichthys, Radiicephalus, Agrostichthys, Regalecus, Trachipterus, Desmodema, Zu) is examined in the second chapter of my dissertation. I used 62 morphological characters from across the ontogenetic continuum to test proposed hypotheses of genus-level relationships of Trachipteridae and familial monophyly of the Lampridiformes. All lampridiform families were recovered as monophyletic except for the Lophotidae, resulting in Eumecichthys as incertae sedis. The suborder Taeniosomoidei is proposed to reflect the monophyletic clade consisting on long-bodied lampridiforms. Trachipteridae is recovered as monophyletic sister group to Regalecidae. The superfamily Trachipteroidea is proposed to recognize this clade. However, within the Trachipteridae, a monophyletic clade consisting of Trachipterus + Zu is recovered but with low support.

Individual-based simulation modelling is an excellent method for testing hypotheses, while including realistic and stochastic population parameters. This thesis considers the evolution of dispersal or inbreeding through individual-based simulation modelling. The occurrence of exclusive inbreeding and exclusive outbreeding is found in a number of organisms and are referred to as mixed mating. Mixed mating is suggested to be in response to low levels of inbreeding depression as well as simultaneous inbreeding- and outbreeding depression while intermediately related mating partners are not available. The results of this thesis show that stable mixed mating strategies evolve in the presence of both inbreeding and outbreeding depression, as well as, under conditions where low levels of inbreeding depression are present. Also, inclusive fitness allows higher levels of inbreeding in genetic systems where the mating partners are more related to each other. Dispersal evidently evolves in response to inbreeding depression. A number of other factors, such as local mate competition and the cost of dispersal also influence the rate of dispersal. In addition to these factors, it is shown in this thesis that male dispersal evolves when there is variation in patch sex ratios. Simulation data also supports parent offspring conflict models, as males have reduced dispersal rates when they, rather than their parents, determine the dispersal rate. Population structure is affected by dispersal rates. Using individual-based simulation modelling and various sampling strategies, reveals that few molecular markers, for a few individuals, are sufficient to accurately detect population subdivision, especially when the sub-populations are large. It is, however, indicated that planning prior to sampling are important for proper assessment of population structure. Lastly, molecular data from the pollinating fig wasp Platyscapa awekei reveals that this species suffers from low levels of inbreeding depression. However, when this data are simulated, stable mixed mating did not evolve although it is observed in P. awekei. Sex ratio variation, high local mate competitions and male only broods are therefore suggested to drive male dispersal. It is consequently advantageous to use various techniques to unravel the evolution of a trait and gain insight into the system. / Thesis (PhD)--University of Pretoria, 2009. / Genetics / unrestricted

No description available.

My dissertation addresses two aspects of eukaryotic evolution, (1) the organization of eukaryotic diversity and (2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life. Relaxed molecular clock analyses of this taxon-rich dataset place the origin on eukaryotes in the Paleoproterozoic, and suggest that all of the major lineages of eukaryotes diverged before the Neoproterozoic. This robust scaffold of the tree of eukaryotes is also used to elucidate common themes in genome evolution across eukaryotes. Mapping dynamic genome features onto this tree demonstrates that they are widespread in eukaryotes, and suggests that a common mechanism underlies genome plasticity. Foraminifera, a diverse lineage of marine amoebae, provide a good model system for investigating genome dynamics because they amplify portions of their genome and go through ploidy cycles during their life cycle. Assessment of nuclear dynamics in one species of Foraminifera, Allogromia laticollaris strain CSH, reveals that genome content varies according the life cycle stage and food source, which may differentially impact organismal fitness. The inclusion of diverse microbial eukaryotes enables better resolution of eukaryotic relationships and improves our understanding the dynamic nature of eukaryotic genomes.

Small bacterial genomes are believed to be evolutionarily derived from larger genomes through massive loss of genes and are usually associated with symbiotic or pathogenic lifestyles. It is therefore intriguing that a similar phenomenon of genome reduction has been reported within a group of free-living phototrophic marine cyanobacteria Prochlorococcus. Here I have investigated the roles of natural selection and mutation rate in the process of Prochlorococcus genome size reduction. Using a data set of complete cyanobacterial genomes including 12 Prochlorococcus and a sister group of 5 marine Synechococcus , I first reconstructed the steps leading to Prochlorococcus genome reduction in a phylogenetic context. The result reveals that small genome sizes within Prochlorococcus were largely determined by massive gene loss shortly after the split of Prochlorococcus and Synechococcus (a process we refer to as early genome reduction). A maximum likelihood approach was then used to estimate changes in both selection effect and mutation rate in the evolutionary history of Prochlorococcus. I also examined the effect of selection and functional importance of a subset of ancestor-derived genes those are lost in Prochlorococcus but are still retained in the genomes of its sister Synechococcus group. It appears that the effect of purifying selection was strongest when a large number of small effect genes were deleted from nearly all functional categories. And during this period, mutation rate also accelerated. Based on these results, I propose that shortly after Prochlorococcus diverged from its common ancestor with marine Synechococcus, its population size increased quickly and thus the efficacy of selection became very high. Due to limited nutrients and relatively constant environment, selection favored a streamlined genome for maximum economies in material and energy, causing subsequent reduction in genome size and possibly also contributing to the observed higher mutation rate.