Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Historical vicariant processes due to glaciations, resulting from the large-scale environmental changes during the Pleistocene (0.012-2.6 million years ago, Mya), have had significant impacts on the geographic distribution of species, especially also in marine systems. The motivation for this study was to provide novel information that would enhance ongoing efforts to understand the patterns of biodiversity on the South African coast and to infer the abiotic processes that played a role in shaping the evolution of taxa confined to this region. The principal objective of this study was to explore the effect of Pleistocene climate changes on South Africa′s marine biodiversity using five intertidal gastropods (comprising four rocky shore species Turbo sarmaticus, Oxystele sinensis, Oxystele tigrina, Oxystele variegata, and one sandy shore species Bullia rhodostoma) as indicator species. Sequence data obtained from partial segments of the mitochondrial cytochrome oxidase c subunit 1 (COI), and the nuclear ribosomal DNA (encompassing part of 5.8S, second Internal Transcribed Spacer and part of 28S, hereinafter called ITS2; or comprising part of the first Internal Transcribed Spacer, 5.8S, second Internal Transcribed Spacer and part of 28S, hereinafter called ITS), were used as genetic markers to construct phylogeographic patterns and to investigate demographic histories of the taxa. Population structure was investigated using haplotype network analyses, pairwise ΦST statistics, analysis of molecular variance (AMOVA), isolation by distance analyses, Bayesian analysis of population structure (BAPS) and coalescent analysis of gene flow. Demographic history was analysed through Fu′s Fs tests, mismatch distributions, and Bayesian skyline plots. Demographic analyses suggest that all five intertidal gastropods studied experienced demographic expansions dating to the late Pleistocene. The sandy shore direct developer B. rhodostoma began expansion after the LGM (c. 15 kya) whereas for the four rocky shore broadcast spawners (T. sarmaticus, O. sinensis, O. tigrina, and O. variegata) the onset of expansion coincided with or preceded the LGM (c. 25, 60, 50, 40 kya, respectively). Consistent with recent range expansions and gene flow patterns, the population genetic structure in all species was characterised by shallow or a lack of population differentiation. Oxystele variegata was an exception as it showed a deep disjunction, of late Pleistocene origin, between individuals in the west coast Namaqua Bioregion and those in the south coast Agulhas Bioregion. These results provide strong evidence of the vital role that Pleistocene climatic changes and current regimes played in shaping the nature and distribution of biodiversity on the South African coast. In addition, gene flow in all species, except O. tigrina, was remarkably asymmetrical with the regions around Cape Infanta and Port Elizabeth acting as source populations. Considering the generally weak population genetic structure and gene flow patterns detected for most gastropod species studied here, it is recommended that T. sarmaticus, O. sinensis, O. tigrina and B. rhodostoma be managed as panmictic populations, and that the region encompassing Cape Infanta, and Port Elizabeth should be prioritised for conservation as it appears to harbour source populations. Oxystele variegata was the only species showing distinct population structure and in this instance, species specific conservation efforts should recognize this divergence by treating the two genetic assemblages as distinct management units. / AFRIKAANSE OPSOMMING: Historiese vikariante prosesse kan toegeskryf word aan glasiasie, en het tot gevolg gehad dat grootskaalse veranderinge in die omgewing plaasgevind het tydens die Pleistoseen (,012 - 2.6 miljoen jaar gelede, Mjg). Dit het 'n beduidende impak gehad op die geografiese verspreiding van spesies, veral ook in die mariene stelsels. Die motivering vir hierdie studie was om nuwe data te voorsien wat sal bydrae tot die voortgesette pogings om die patrone van biodiversiteit langs die Suid-Afrikaanse kus te verstaan. Dit sou ook help om die abiotiese prosesse af te lei wat 'n rol gespeel het in die evolusie van taksa wat in hierdie streek voorkom. Die hoofdoel van hierdie studie was om die effek van die Pleistoseen klimaatsveranderinge op Suid-Afrika se mariene biodiversiteit te bepaal deur gebruik te maak van vyf intergety slak spesies as indikatore (vier wat in rotsagtige gebiede voorkom: Turbo sarmaticus, Oxystele sinensis, Oxystele tigrina, Oxystele variegata en 'n sanderige strand spesies: Bullia rhodostoma). Volgorde data verkry vanaf gedeeltelike segmente van die mitochondriale sitochroom oksidase c subeenheid 1 (COI), en die kern ribosomale DNA (bestaande uit 'n deel van 5.8S, tweede interne getranskribeerde spasieërders en 'n deel van 28S), hierna genoem ITS2 is gebruik as genetiese merkers om filogeografiese patrone te dokumenteer en ook om die demografiese geskiedenis van die spesies te ondersoek. Bevolking struktuur is ondersoek deur gebruik te maak van haplotipe netwerk analise, paarsgewyse ΦST statistiek, analise van molekulêre variansie (AMOVA), isolasie deur afstand analise, Bayesiaanse analise van die bevolking struktuur (BAPS) en analise van gene vloei. Demografiese geskiedenis is ontleed deur Fu se Fs toetse, misparing verdelings, en Bayesiaanse luglyn kurwes. Demografiese ontleding dui daarop dat al vyf die intergety slakke wat ondersoek is demografiese uitbreidings ervaar het wat terugdateer tot die einde van die Pleistoseen. Die sanderige strand direkte ontwikkelaar, B. rhodostoma, het die uitbreiding begin na die LGM (c. 15 Kya), terwyl vir die vier rotsagtige kusbewoners wat eiers oor 'n uitgebreide gebiede versprei (T. sarmaticus, O. sinensis, O. tigrina, en O. variegata) het die aanvang van die bevolkings uitbreiding saamgeval met die laaste galsiasie of dit voorafgegaan (c. 25, 60, 50, 40 Kya, onderskeidelik). In ooreenstemming met die onlangse reeks bevolkings uitbreidings, is die bevolking genetiese struktuur in alle spesies gekenmerk deur weinig differensiasie. Oxystele variegata was 'n uitsondering en het 'n ontwrigting van laat Pleistoceen oorsprong getoon tussen individue langs die weskus Namaqua Biostreek en dié in die suid kus Agulhas biostreek. Hierdie resultate voorsien sterk bewyse van die belangrike rol wat die Pleistoseen klimaatsveranderinge gespeel het in die vorming en verspreiding van biodiversiteit langs die Suid-Afrikaanse kus. Daarbenewens, geen vloei in alle spesies, behalwe O. tigrina, was merkwaardig asimmetries. Kaap Infanta en Port Elizabeth verteenwoordig moontlik die bron bevolkings. Met inagneming van die geringe bevolking genetiese struktuur en geenvloei patrone wat waargeneem is vir die meeste slak spesies wat bestudeer is, word dit aanbeveel dat T. sarmaticus, O. sinensis, O. tigrina en B. rhodostoma bestuur word as 'n panmiktiese bevolking, en dat die streek wat Kaap Infanta en Port Elizabeth insluit geprioritiseer moet word vir bewaring. Oxystele variegata was die enigste spesie wat duidelike bevolking struktuur getoon het en in hierdie geval, moet spesie spesifieke bewaringspogings aangewend word.

This work examines the use of pedo-properties to identify dune soil system responses to environmental change on the Sefton coast, based on the development of conceptual pedogenic models. Previous environmental change and shoreline dynamics are determined through O.S. maps and aerial photographs, while present day processes are investigated through a dune-toe photographic survey and seasonal monitoring by fixed point photography. Topsoil (0-5 cm) physico-chemical characteristics are presented in a series of baseline GIS maps, displaying spatial pedo-property variation across the dune landscape. Combined with vegetation data, topsoil analysis identifies 10 distinct pedo-environments. Physico-chemical characteristics of associated National Soil Resources Institute (NSRI) soil profile classifications and an exposed stratigraphic section are presented graphically in a proposed sequence of development. Topsoil and soil profile samples are analysed for soil pH, soil organic matter (SOM) content, particle size, geochemical composition and mineral magnetism. Significant differences (p <0.05) are apparent for the suite of topsoil characteristics collated, indicating discrete dune environments are influenced by specific soil properties. Distinct down-profile variations in soil characteristics are also apparent between dune environments, highlighting pedological dynamism. Multivariate Factor analysis groups bare sand and mobile dune communities into ‘frontal dunes’ and fixed dune community, pasture, scrub, deciduous woodland and coniferous plantations into ‘hind dunes’, separating these topsoil environments from heath and slack communities. Factor analysis also identifies linkages between pedo-characteristics within soil profile horizons, suggesting pedogenesis on the Sefton dunes initiates as raw sand, progressing to sand-pararendzinas through leaching of nutrients. Desalinization and decalcification processes lead to brown earth development, followed by increased acidicification, subsequently, resulting in micro-podzol formation. Groundwater gley soils are associated with dune slacks, where drainage is inhibited and anaerobic conditions prevail. Analysis of buried soils suggests such pedo-environment formations are cyclic, responding to phases of shoreline regression/transgression, dune activity and stabilization. Conceptual models are designed to graphically demonstrate pedogenesis under both erosion and deposition regimes on the Sefton coast. Regression equations and correlation coefficients between pedo-properties and distance from mean high water are used as a proxy for soil age, which represent lateral soil maturity from the unstable frontal dunes to the stable hind dunes inland. The models simulate formation and process of the full array of soil properties, accounting for geomorphological impacts and anthropogenic influences. This has great implications for dune managers by raising awareness of pedogenesis as an integral part of nature and associated habitats, which could be incorporated in future shoreline management plans (SMPs).

published_or_final_version / Geography and Geology / Doctoral / Doctor of Philosophy

published_or_final_version / History / Master / Master of Philosophy

The customer service within the United States Coast Guard Naval Engineering department has increased significantly in the past decade. Many areas of the naval engineering departments have adopted a customer service policy in part or in whole. However, the naval engineering community is persistently working to reduce costs and operational liabilities generated through their support practices. Financial and operational liabilities have also grown in the past decade, and the United States Coast Guard Naval Engineering department has failed to aggressively address this issue until recently. This leaves naval engineering communities who use their own version of customer service policies to adopt a standard that is compliant toward the Coast Guard’s Naval Engineering force management goals. This paper looks at the history of Coast Guard Naval Engineering customer service issues, how the engineering community has managed the issues in the past and how improvements can be made. / text

Expanding groundfish production on the West Coast and in the United States in total, over the past decade, has increased competition in the groundfish market. During the same period, regulations have evolved to control production in the groundfish industry for the purpose of conserving the resource. Other regulations exist to control certain aspects of the market for groundfish. Such regulations are generally expected to have local impacts. However, little consideration is usually given to the impact regulations may have outside a local area. Indeed, since market competition has increased so significantly in this industry, the geographical distribution area has expanded considerably in recent years. Inter-regional impacts should be considered when regulations are established. The purpose of this research was to examine the impact selected regulations may have on markets for groundfish. The hypothesis tested by this research is stated as the following: regulations intended to impact local regions have no more than a local affect. Stated another way, regulatory authorities at state or regional levels generally intend to impose regulations that do not impact regions other than those under their jurisdiction. The test, then, is to determine if other regions are affected by "localized" regulations. The regulations to be examined include restriction or alteration of production in a limited region and established intra-state transportation rates (for seafood) that limit competition in the state transportation market. Specifically, alternative distribution patterns were generated in response to postulated changes in: (1) the availability of groundfish in the Oregon region and (2) California intra-state transportation rates to reflect more competition in the seafood transportation market (lower rates). The hypothesis was tested by estimating demand equations for groundfish, employing these in a spatial equilibrium model, and subjecting the results to a sensitivity analysis. The hypothesis testing consists of four parts, each independently insufficient to reject the hypothesis. As a whole, however, the four parts should provide enough evidence (although not a statistical test) to reject the hypothesis. The results of the research indicate rejection of the hypothesis was acceptable. Indeed, several of the regions where no affect was expected in response to the postulated changes showed significant impacts. This research was a pioneering attempt. The results are not conclusive, in part because of the absence of appropriate data. However, the results were significant enough to indicate promising possibilities for future research. In fact, a major contribution of the work was to point out how this research technique can be improved by refining inputs to the model and increasing its complexity to reflect more of the available routes associated with different product forms, product transport techniques and different species. The major result of the research was to indicate the need to consider impacts which extend beyond the local market in establishing regulations. / Graduation date: 1986

Sediment deposit ages inferred from radiocarbon dating of stream bank material were used to estimate residence times of valley-floor deposits in headwater valleys of the Oregon Coast Range, USA. Inherited ages of radiocarbon-dated material, i.e., time between carbon fixation in wood and its incorporation in a sediment deposit, can result in over-estimation of the ages of those deposits and, hence, the residence times of sediment within those units. Calibrated radiocarbon dates of 126 charcoal pieces sampled from Knowles Creek were used to estimate the distribution of inherited ages in fourteen depositional units representing three deposit types: fluvial fines, fluvial gravels, and debris flows. Within a depositional unit, the inherited age distribution of a piece of charcoal was estimated by convolving its calibrated age distribution with that of the piece of charcoal with the smallest weighted-mean calibrated age (i.e., an approximation of a unit's date of deposition) within that unit. All inherited age distributions for a particular deposit type were then added and normalized to provide a probability distribution of inherited ages for that deposit type. Probability distributions of inherited ages average 688, 1506, and 666 yr for fluvial fines, fluvial gravels, and debris flow units, respectively. Curves were fit to inherited age distributions for each deposit type. These curve fits were then convolved with deposit age distributions (i.e., equal to calibrated age distributions of woody material sampled from stream banks) of samples from Bear Creek (Lancaster and Casebeer, 2007) to correct these deposit ages for inherited age. This convolution gives a corrected deposit age. In cases in which means of corrected deposit age distributions for an upper unit were older than those of a lower unit within a stratigraphic column, the upper sample’s corrected deposit age distribution was set to that of the youngest lower in the stratigraphic section. Convolution shifted individual deposit age distributions towards zero and increased their standard deviation by an average of 365%. However, convolution decreased the standard deviations of normalized probability distribution functions of deposit ages inferred from many samples from 1340 to 1197 yr, and from 471 to 416 yr for lower and upper reaches, respectively, of the Bear Creek valley in the Oregon Coast Range. Convolution decreased estimates of mean deposit ages from 1296 to 1051 yr, and from 308 to 245 yr for lower and upper reaches, respectively, of the Bear Creek. Estimates of percentages of basin denudation passing through each reach's deposit ("trapping efficiency") increased from 11.6% to 14.4%, and from 25.4% to 31.9% for lower and upper Bear Creek, respectively. However, basic shapes of residence time distributions and, thus, inferences regarding removal of sediment from the reaches did not change after deposit dates were corrected. Sediment residence times in the lower Bear Creek valley are exponentially distributed, which implies that all sediment has a uniform probability of evacuation from deposits, whereas the power-law-distributed residence times in upper Bear imply preferential evacuation of younger deposits and preservation of older deposits. Much of the sediment transported onto valley floors via debris flows is deposited, and then is evacuated over longer times. Volumes and residence times of stored sediment in these deposits at the transition from debris flow to fluvial evacuation, and their associated width of valley floors, vary throughout a network. Export volumes and frequencies from tributaries are controls on deposit volumes and may control valley widening of mainstem valley floors. In addition, closely spaced tributaries may exert composite effects on valley floor landforms. It is hypothesized that the volumes of sediment stored at confluences increases with contributing watershed area of tributaries to the point where tributary slopes are low enough to cause most debris flows to be deposited within tributary valleys instead of in the mainstem valley. In four ~1 km reaches with contributing watershed areas of 0.3 to 5.0 km², field surveys provided measures of width of valley floors and volume of deposits, and radiocarbon dating of charcoal provided residence times of sediment in these deposits. Mean residence times of reaches vary between 1.1 and 2.5 kyr. Exponential distributions fit to residence times within two of the reaches imply evacuation of sediment independent of deposit ages. Power-law fits to residence times of the other two reaches imply age-dependent evacuation of deposits. Distribution shapes of residence times, and their means, do not vary systematically with contributing watershed area of mainstems. Mean width of mainstem valley floors increases with contributing watershed areas of both mainstems and their respective tributaries. Volumes of sediment stored on the valley floor increase with contributing areas of mainstems, and these volumes at tributary junctions peaked at tributary contributing areas of ~0.1 km². Percentage of basin denudation entering storage decreases with contributing area of mainstem. This decrease may be due to increasing percentages of sediment supply via fluvial transport for larger watersheds, and much, if not most, of this supply routes through the system quickly. / Graduation date: 2012

The American Cordillera, a major mountain belt spanning>15000 km along the western margins of North and South America, formed as a result of crustal shortening and magmatism during ocean-continent convergence. These mountains were the loci of addition and redistribution of continental crust. The contributions presented here address the style, timing, and kinematics of underthrusting of continental crust in the retroarc of the central Andes as well as the rapid burial and metamorphism of forearc rocks that contributed to magmatism in the Canadian Cordillera. This work involved geological mapping and structural analysis coupled with geo- and thermochronological analysis. In the central Andes, results confirm a southward transition in structural style and magnitude of Cenozoic shortening that coincides with the disappearance of a thick Paleozoic basin that accommodated major Cenozoic shortening. U-Pb and (U-Th)/He results also demonstrate that thrust belt kinematics in northwestern Argentina were greatly influenced by pre-orogenic heterogeneities in Cretaceous rift architecture. Results from western Canada reveal that rapid underthrusting of forearc rocks occurred during Late Cretaceous time, likely associated with an episode of shallow subduction. This event did not result in basement-involved foreland uplifts thought to be a signature of shallow subduction in the western United States and central Argentina. Taken together, this work has the major implication that variations in the pre-orogenic upper crustal architecture strongly influence the behavior of the continental lithosphere during orogenesis, a result that challenges geodynamic models that largely neglect upper plate heterogeneities.

Accelerated glacial recession and downwasting of glaciers in the Bowser River Watershed of the northern British Columbia Coast Mountains have exposed subfossil wood remains and laterally contiguous wood mat layers. To develop an understanding of Holocene glacial fluctuations in this region, field investigations were conducted in 2005, 2006 and 2013 at Frank Mackie, Charlie, Salmon and Canoe glaciers. These wood remains represent periods of Holocene glacier advance, when glaciers expanded and overwhelmed downvalley forests. Dendroglaciology and radiocarbon analyses revealed five intervals of glacial expansion: (1) a mid-Holocene advance at 5.7-5.1 ka cal. yr BP; (2) an early Tiedemann advance at 3.6-3.4 ka cal. yr BP; (3) a late Tiedemann advance at 2.7-2.4 ka cal. yr BP; (4) a First Millennium AD Advance at 1.8-1.6 ka cal. yr BP; and, (5) three advances during the Little Ice Age at 0.9-0.7, 0.5 and 0.2-0.1 ka cal. yr BP. These results provide new evidence for mid-Holocene glacier activity in northern British Columbia, as well as supporting previous research that Holocene glacier advances were episodic and regionally synchronous. / Graduate / 0368

The main goal of this thesis was to develop a multi-technique approach to characterise high molecular weight (colloidal) dissolved organic matter (DOM) occurring in estuarine and coastal marine environments and to investigate how these bulk properties may relate to their ability to influence the physicochemical speciation of metals such as iron and copper. This characterisation was undertaken systematically on the pre-filtered (0.4 μm) estuarine or marine sample, referred to here as the ‘bulk’, as well as on the ultrafiltered (< 5 kDa) and colloidal (> 5 kDa) fractions. Three successive studies were carried out. The first one took place in the estuarine mixing zone of a high pH, low turbidity black water river (River Thurso) and the other two in the receiving coastal waters (Thurso Bay). The optical and size distribution properties of these waters were examined in detail in the first study while their iron and copper-binding properties were examined in the second and third studies, respectively. Size fractionation results showed that the proportion of colloidal to soluble organic carbon (DOC) tended to decrease from the upper estuary (~ 60%) to coastal waters (~ 20%). With respect to trace metals, similar trends were observed as one progressed from the mouth of the river towards the open sea. In relation to their molecular absorption, fluorescence and size fractionation properties, both River Thurso DOM and Nordic Reservoir NOM Reference Material presented the same characteristics and mixing behaviour, indicating the dominance of humic and fulvic substances in the Thurso river-ocean system. The river-borne, humic colloids underwent two types of transformations upon mixing with the seawater end-member. The first one was the coiling or contraction of individual macromolecules ―monomers― with increasing salinity. The second one was the concurrent aggregation of these small monomer units (d = 2 – 4 nm) to form entities that were still colloidal, i.e. smaller than 0.4 μm. As a result of extensive association of iron and copper with the colloidal and soluble fractions respectively, not only organic carbon but also iron and copper behave conservatively in the River Thurso estuary. Throughout the coastal region of freshwater influence (S = 29 - 35) colloidal iron accounted for 30 - 80% of total dissolved iron and was present as iron-humic complexes supplied by the river and showing a uniform stability constant (log KFe’HS’ = 11.3  0.1, i.e. log KFe3+ HS’ = 21.3  0.1). Soluble iron was found to be largely complexed to ligands of marine origin with log K’Fe’HS’ = 11.9  0.1, thus revealing for the first time a difference between the iron-binding strengths of colloidal and soluble ligands. Terrestrial colloidal iron was found to be entirely, if slowly (~ 10 hours), accessible to the added competing ligand 2-(2-thiazolylazo)-pcresol (TAC) used for the determination of K’Fe’HS’. Furthermore, iron appeared to play a role in holding these terrestrial colloids together. Evidence for this came from variations in humic fluorescence intensity over time in response to dissociation of the ironhumic colloidal associations induced by a chelating resin. These results are consistent with the concept that iron derived from a peat-draining river is strongly but reversibly bound to humic substances and remains so under marine conditions. In the same coastal region, two types of high-affinity ligands binding over 99.99% of total copper were detected. The stronger ligand (L1, log KCu2+L1’ = 15.5 - 16.1), of riverine origin, was present in very low concentrations of 1 - 4 nM that correlated with ―but systematically fell short of― total copper concentrations. Its conditional binding constant tended to increase with salinity, with most of the increase taking place in the near-field portion of the river plume. The weaker, more abundant ligand (L2, log KCu2+L2’ = 11.8 - 12.8) was present in total concentrations of 60 – 170 nM and had a controlling influence on the value of the labile (i.e. inorganic) copper concentration which ranged from 0.001 to 0.0001 nM. Both organic ligands were fairly evenly partitioned between soluble and colloidal phases but their sources appeared to differ significantly. Ligand L1 appeared to be of riverine origin (although one cannot exclude active microbial production, as opposed to passive release from peat) while ligand L2 distributions suggested in situ production within Thurso Bay.