Genomic sequence data from the three domains of life have revealed a remarkable diversity of genome architectures. The relative contributions of adaptive versus non-adaptive processes in shaping this diversity are poorly understood and hotly debated. This thesis investigates the evolution of genome architecture in the Chloroplastida (i.e., green algae and land plants), with a particular focus on the mitochondrial and plastid genomes of chlamydomonadalean algae (Chlorophyceae, Chlorophyta). Much of the work presented here describes unprecedented extremes in: i) genome compactness (i.e., the fraction of noncoding DNA in a genome), ii) genome conformation (e.g., circular vs. linear vs. linear fragmented genomes), iii) intron and repeat content; and iv) nucleotide-composition landscape (e.g., GC-rich vs. AT-rich genomes). These data are then combined with intra-population nucleotide diversity data to explore the degree to which non-adaptive forces, such as random genetic drift and mutation rate, have shaped the organelle and nuclear genomes of the Chloroplastida. The major conclusions from this dissertation are that chlamydomonadalean algae show a much greater variation in organelle genome architecture than previously thought — this group boasts some of the most unusual mitochondrial and plastid genomes from all eukaryotes — and that the majority of this variation can be explained in non-adaptive terms.

No description available.

No description available.

Geographic variation was analysed in morphological (colour, morphometric) and genetic (electrophoretic, chromosomal) characters in the yellow mongoose cynictis penicillata, a diurnal, colonial, burrow-dwelling viverrid, endemic to and widespread throughout Southern Africa. The causal bases of observed geographic patterns were investigated, and a taxonomic revision of the species was undertaken. Three physical properties of pelage colour (hue, value and chroma) were measured independently using Munsell colour charts and a tristimulus colorimeter. Hue and chroma varied from yellowish (hue) and bleached (chroma) in the north to a brighter, (chroma) tawny-orange (hue) in the south. A zone of rapid colour change separated northern and southern groups. Specimens from the drier western areas were paler (in value) than specimens from more easterly localities. Colour patterns were interpreted in terms in the principle of metachromism. Environmental correlates of colour were analysed. Non-geographic (age, sex, individual) and geographic variation was analysed in 14 cranial and two external characters, using multivariate and univariate techniques. The species does not show secondary sexual dimorphism. Multivariate analyses resulted in the description of four parapatric subspecies, three of which were distinguished on the basis of skull size (which accounted for 93% of geographic variation). Subspecies were separated by continuous zones of craniometric differentiation (transition zones). Craniometric overlap (intergradation) occurred across transition zones. The geographic pattern of craniometric variation in C. penicillata could be explained by either an allopatric or a parapatric mode of speciation. A cladistic analysis of coded cranial characters was used to infer the historical pattern of range expansion in the species. The population genetical structure, based on electrophoretic analysis of 28 loci in eight populations of yellow mongooses, was characterised by the absence of genetic divergence between morphometrically-defined subspecies, a mean expected heterozygosity of 3.4%, low genetic distances between populations (0.000--0.105 for Nei's genetic distance), and a surprisingly high fixation index (FST) of 0.585. The basic karyotype of the yellow mongoose was invariant geographically (2n = 36, NF = 72), although a single, supernumerary microchromosome was detected in four out of the five populations sampled. G- and C-banded karyotypes are presented. Evolutionary relationships among eight Southern African viverrid species, including the yellow mongoose, were inferred from phenetic and cladistic analyses of allelic variation at 18 protein loci. These data suggested the separate evolution of social and solitary lineages of mongooses. / Thesis (Ph.D.)-University of Natal, 1990.

Despite considerable progress in recent years, a complete description of the physical drivers of galaxy formation and evolution remains elusive, in part because of our poor understanding of star formation, and how star formation in galaxies is regulated by feedback from supernovae and massive stellar winds. Insight into the star formation histories of galaxies, and the interplay between star formation and feedback, can be gained by measuring their chemical abundances, which until recently has only been possible for galaxies in the nearby universe. However, reliable star formation and abundance calibrations have been hampered by various systematic uncertainties, and the lack of a suitable spectrophotometric sample with which to develop better calibrations. To address the limitations of existing surveys, we have obtained integrated optical spectra for a diverse sample of more than four hundred nearby star-forming galaxies. Using these data, in conjunction with observations from the Sloan Digital Sky Survey, we conduct a detailed analysis of optical star formation indicators, and develop empirical calibrations for the [O II] 3727 and H-beta 4861 nebular emission lines. Next, we investigate whether integrated spectroscopy of star forming galaxies can be used to infer their gas-phase oxygen abundances in the presence of radial abundance gradients, diffuse-ionized gas emission, and dust attenuation. We conclude that the integrated R23 parameter is generally insensitive to these systematic effects, enabling the gas-phase metallicity to be measured with a precision of +/-0.1 dex. We apply these methods to study the evolution in the luminosity-metallicity relation at 0<z<1 based on an analysis of more than 3500 I-band selected galaxies observed as part of the AGN and Galaxy Evolution Survey, and data culled from the literature. Our principal results are that, at fixed luminosity, the mean gas-phase metallicity of luminous (MB<-19 mag), star-forming galaxies at z=1 is a factor of two lower than the gas-phase metallicity in comparably luminous galaxies at z=0. However, after accounting for the effects of luminosity evolution, we find that the amount of chemical evolution for luminous galaxies corresponds to an increase of only 10%-20% since z1⁺ё, assuming a direct evolutionary connection between nearby and distant star-forming galaxies.

The transition between terrestrial varanoid lizards and aquatic mosasaurs through the intermediate, semi-aquatic aigialosaurs is fully documented. Aigialosaurs are shown to possess a mosaic of mosasaurian (configuration of the skull, jaw and tail) and terrestrial varanoid characters (appendicular skeleton and trunk). / The taxonomic position of the Aigialosauridae within the superfamily Varanoidea is evaluated. Based on character states previously used to define the Varanoidea, neither the specific affinities of aigialosaurs nor the sister-group relationships of earlier members of the terrestrial varanoid assemblage can be securely established. For this reason, the specific character states involved have been reexamined and alternative hypotheses of relationship have been considered.

Optical imaging polarimetry has been performed on a small sample of objects which are associated with that stage of stellar evolution occurring between the Asymptotic Giant Branch and full Planetary Nebula. Three such systems are considered, specifically, the young planetary nebulae M 1-16 and Mz3, and the protoplanetary nebula, IRAS 09371+1212 (the 'Frosty Leo' nebula). The work is based upon CCD polarimetry obtained with the Durham Imaging Polarimeter. Planetary nebulae are believed to form as a low to intermediate mass star evolves from the main sequence, through the mass-loss stages of the Red Giant Branch and Asymptotic Giant Branch, towards its final destiny as a White Dwarf. A brief review of the relevant aspects of post-main sequence stellar evolution is given as a basis for understanding the transitionary planetary nebula phase in relation to the character of the central star and its role in the creation of a nebula. The theory of light scattering from both homogeneous and core-mantle spherical dust grains (Mie theory) is discussed. The results of a series of scattering calculations, using the theory, for dust grains composed of those materials believed to be abundant in the atmospheres of late-type stars and planetary nebulae are presented. The levels of polarization and scattered intensities predicted in the scattering analysis have been applied in the interpretation of the polarimetric data for the three planetary nebulae. Constraints upon the nature of the dust component, the size distribution of the dust and the nebula geometry are suggested for each of the nebulae. The inferred character of the dust material is in good agreement with the classification of the nebulae using the two-colour diagram for the IRAS fluxes.

Software development projects typically involve repeated interactions among several groups of people. This setting seems well suited for an analysis by means of the standard-model of the evolution of cooperation, the Iterated Prisoner's Dilemma. Computer simulations of a population of stochastic reactive strategies show that the existence of intergroup discrimination can be modeled endogeneously as a result of noise due to misperception of the opponent's move. (author's abstract) / Series: Working Papers on Information Systems, Information Business and Operations

This thesis examines Escherichia coli pyruvate kinase type 1 (PK1), a regulatory enzyme core to energy metabolism. Specifically, this thesis characterises a series of mutations in PK1 that were found when populations of E. coli were evolved in a glucose-limited environment for 20,000 generations. The gene pykF, which codes for the PK1 enzyme, was found to have developed nonsynonymous mutations in all replicate populations. Although the mutations at the nucleotide level were not the same (i.e. not parallel), it is not clear whether parallel adaptation exists at the protein structure/function level. This study aimed to address this question by investigating the kinetic and biophysical properties of the wild-type and seven mutant enzymes. The recombinant wild-type PK1 enzyme used in this study was found to have steady state kinetics consistent with those previously reported. Unlike the rabbit kidney PK enzyme, E. coli PK1 was shown to have a very tight tetrameric structure (picomolar range), which was not affected by the enzyme’s substrates (PEP and ADP), or the allosteric effector (FBP), as judged by analytical ultracentrifugation with fluorescence detection. The mutated residues were highly conserved, and found to fall loosely into three groups: those at the active site (P70T, P70Q and D127N); those at the subunit interface (I264F, A301T and A301S); and at the allosteric binding site (G381A). The seven mutated PK1 enzymes were obtained by mutagenesis followed by protein purification. Steady state kinetic analysis showed that the mutated enzymes displayed a variety of functional changes, suggesting that the populations had not evolved in a parallel manner at the enzyme structure/function level. Mutations within the active site (P70T, P70Q and D127N) all showed a decrease in catalytic potency. P70 is located at the hinge connecting the A and B domains, which forms the active site. PK1-P70Q showed strong cooperative binding to PEP, similar to the wild-type enzyme, in the absence of FBP, whereas PK1-P70T had little cooperativity, suggesting changes in the active site. PK1-D127N showed severely attenuated activity, suggesting, for the first time, that this residue is essential for catalysis. Mutations at the subunit interface (I264F, A301T and A301S) all showed altered allosteric regulation, suggesting that this interface is important in the FBP allosteric response. PK1-I264F, which had lower activity, but greater affinity for PEP, displayed a decreased α-helix content (as judged by CD), indicating that a subunit interface helix that includes this residue had altered. Despite still having a similar response to FBP, PK1-G381A showed an increased affinity for PEP, which, together with an increased α-helix content, suggests that this mutation had changed the structure of the FBP binding domain. None of the mutated enzymes showed altered quaternary structure. Although the populations evolved parallel changes with respect to cell physiology, fitness, and gene expression, this study suggests, for the first time, that the populations have not evolved in a parallel way with respect to protein structure and function.

This PhD dissertation is focused on short tandemly repeated nucleotide patterns which occur extremely often across DNA sequences, called microsatellites. The main characteristic of microsatellites, and probably the reason why they are so abundant across genomes, is the extremely high frequency of specific replication errors occurring within their sequences, which usually cause addition or deletion of one or more complete tandem repeat units. Due to these errors, frequent fluctuations in the number of repetitive units can be observed among cellular and organismal generations. The molecular mechanisms as well as the consequences of these microsatellite mutations, both, on a generational as well as on an evolutionary scale, have sparked debate and controversy among the scientific community. Furthermore, the bioinformatic approaches used to study microsatellites and the ways microsatellites are referred to in the general literature are often not rigurous, leading to misinterpretations and inconsistencies among studies. As an introduction to this complex topic, in Chapter I I present a review of the knowledge accumulated on microsatellites during the past two decades. A major part of this chapter has been published in the Encyclopedia of Life Sciences in a Chapter about microsatellite evolution (see Publication 1 in Appendix II). The ongoing controversy about the rates and patterns of microsatellite mutation was evident to me since before starting this PhD thesis. However, the subtler problems inherent to the computational analyses of microsatellites within genomes only became apparent when retrieving information on microsatellite distribution and abundance for the design of comparative genomic analyses. There are numerous publications analyzing the microsatellite content of genomes but, in most cases, the results presented can neither be reliably compared nor reproduced, mainly due to the lack of details on the microsatellite search process (particularly the program’s algorithm and the search parameters used) and because the results are expressed in terms that are relative to the search process (i.e. measures based on the absolute number of microsatellites). Therefore, in Chapter II I present a critical review of all available software tools designed to scan DNA sequences for microsatellites. My aim in undertaking this review was to assess the comparability of search results among microsatellite programs, and to identify the programs most suitable for the generation of microsatellite datasets for a thorough and reproducible comparative analysis of microsatellite content among genomic sequences. Using sequence data where the number and types of microsatellites were empirical know I compared the ability of 19 programs to accurately identify and report microsatellites. I then chose the two programs which, based on the algorithm and its parameters as well as the output informativity, offered the information most suitable for biological interpretation, while also reflecting as close as possible the microsatellite content of the test files. From the analysis of microsatellite search results generated by the various programs available, it became apparent that the program’s search parameters, which are specified by the user in order to define the microsatellite characteristics to the program, influence dramatically the resulting datasets. This is especially true for programs suited to allow imperfections within tandem repeats, because imperfect repetitions can not be defined accurately as is the case for perfect ones, and because several different algorithms have been proposed to address this problem. The detection of approximate microsatellites is, however, essential for the study of microsatellite evolution and for comparative analyses based on microsatellites. It is now well accepted that small deviations from perfect tandem repeat structure are common within microsatellites and larger repeats, and a number of different algorithms have been developed to confront the challenge of finding and registering microsatellites with all expectable kinds of imperfection. However, biologists have still to apply these tools to their full potential. In biological analyses single tandem repeat hits are consistently interpreted as isolated and independent repeats. This interpretation also depends on the search strategy used to report the microsatellites in DNA sequences and, therefore, I was particularly interested in the capacity of repeat finding programs to report imperfect microsatellites allowing interpretations that are useful in a biological sense. After analzying a series of tandem repeat finding programs I optimized my microsatellite searches to yield the best possible datasets for assessing and comparing the degree of imperfection of microsatellites among different genomes (Chapter III) During the program comparisons performed in Chapter II, I show that the most critical search parameter influencing microsatellite search results is the minimum length threshold. Biologically speaking, there is no consensus with respect to the minimum length, beyond which a short tandem repeat is expected to become prone to microsatellite-like mutations. Usually, a single absolute value of ~12 nucleotides is assigned irrespective of motif length.. In other cases thresholds are assigned in terms of number of repeat units (i.e. 3 to 5 repeats or more), which are better applied individually for each motif. The variation in these thresholds is considerable and not always justifiable. In addition, any current minimum length measures are likely naïve because it is clear that different microsatellite motifs undergo replication slippage at different length thresholds. Therefore, in Chapter III, I apply two probabilistic models to predict the minimum length at which microsatellites of varying motif types become overrepresented in different genomes based on the individual oligonucleotide frequency data of these genomes. Finally, after a range of optimizations and critical analyses, I performed a preliminary analysis of microsatellite abundance among 24 high quality complete eukaryotic genomes, including also 8 prokaryotic and 5 archaeal genomes for contrast. The availability of the methodologies and the microsatellite datasets generated in this project will allow informed formulation of questions for more specific genome research, either about microsatellites, or about other genomic features microsatellites could influence. These datasets are what I would have needed at the beginning of my PhD to support my experimental design, and are essential for the adequate data interpretation of microsatellite data in the context of the major evolutionary units; chromosomes and genomes.