<p> <i>Arabidopsis thaliana</i> has undergone three whole genome duplications within its ancestry, and these events have dramatically affected its gene complement. Of the most recent whole genome duplication events (&alpha; event), there remain 11,452 conserved noncoding sequences (CNSs) that have been retained proximal to &alpha; duplicate gene pairs. As functional DNA elements are expected to diverge in sequence at a slower rate than nonfunctional DNA elements, the retained CNSs likely encode gene regulatory function. Within this dissertation I provide evidence for the regulatory role of CNSs within <i> Arabidopsis thaliana</i>. Using a collection of over 5,000 microarray RNA expression profiling datasets, I demonstrate that the presence of CNSs near &alpha; duplicate pairs is correlated with changes in average expression intensity (AEI), &alpha; duplicate pair co-expression, mRNA stability, and breadth of gene expression. The effects of CNSs on AEI, co-expression, and mRNA stability vary relative to their subgene position, because they are located in nontranscribed (5&rsquo;-upstream and 3&rsquo;-downstream) and transcribed (5&rsquo;- UTR, intronic and 3&rsquo;-UTR) regions. Modeling gene interactions through the generation of co-expression networks, I also demonstrate that a portion of CNSs participate in known gene regulatory networks. Collectively, this body of work demonstrates that CNSs regulate steady-state mRNA levels within Arabidopsis thailiana through both transcriptional and post-transcriptional mechanisms.</p>

This work presents detailed analysis from the GEEC2 spectroscopic survey of galaxy groups at 0.8<z<1. This deep survey, which has a magnitude limit of r_AB<24.75, had previously found a population of intermediate ('green') galaxies between the star-forming ('blue') and quiescent ('red') sequences. GMOS-S spectroscopy for the 11 X-ray selected galaxy groups was obtained and is highly complete ( > 66 per cent) for eight of the eleven groups. Using an optical-NIR colour-colour diagram, the galaxies in the sample are separated with a dust insensitive method into the three categories, star-forming, quiescent, and intermediate. The strongest environmental dependence is observed in the fraction of quiescent galaxies, which is higher inside groups than in the field for all stellar masses. While intermediate galaxies represent ~15-20 per cent of the star-forming population in both the group and field, the average specific star formation rates (sSFR) of the group population is lower by a factor of ~3. The intermediate population also does not show the strong Hδ absorption that is characteristic of starburst galaxies. Inside groups, only 4.4-6.7 per cent of star-forming galaxies are starbursts, which gives additional validity to the assumption that the quenching of star-formation is the primary process in the transition from the star-forming to the quiescent state. With the use of stellar synthesis models, two possible scenarios for the origins of the intermediate population are investigated, including the quenching of star-forming galaxies via environmental processes and the rejuvenation of star formation in early-type galaxies via mixed mergers. To model the quenching scenario, we have tested the use of different exponential quenching timescales (τ_2) and different types of delays between satellite accretion and the onset of quenching. We found that the fraction of intermediate galaxies depends most strongly on the value of τ_2. The relative fractions of galaxies rule out both the no-delay scenario, which would require a long τ_2 that over-produces intermediate galaxies, as well as the constant 3 Gyr delay model, which does not produce a sufficient number of quiescent galaxies. The observed fractions are best matched with a model that includes a dynamical delay time and a τ_2=0.25 Gyr, but this model also predicts intermediate galaxies Hδ strength higher than that observed. For the rejuvenation scenario, we found that the time visible in the intermediate region is directly related to the size of the second 'burst' of star-formation, which can then be further constrained by the Hδ strength for the intermediate population. The observations are best matched to a burst size of ~1 per cent, at a rate of ~3 times per Gyr. In order to properly distinguish between the two scenarios, we will need to both increase the signal-to-noise ratio for the Hδ measurements and conduct a deeper survey of satellite galaxies both inside groups and in the field.

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