Scarabaeus (Pachysoma) consists of 13 flightless dung beetle species endemic to the arid west coast of southern Africa. Scarabaeus (Pachysoma) are unique in their feeding and foraging habits, in that they randomly search for dry dung/detritus which, when found, is dragged forwards, and buried in a pre-constructed holding chamber, as opposed to the convention of rolling it backwards. This action is repeated to provision the chamber after which the nest is expanded to below the moisture line to allow the stored food to re-hydrate. Poor vagility, taxonomic contention - seen in Scarabaeus taxonomy - and conservation concern, made Scarabaeus (Pachysoma) an ideal group of beetles to study both the phylogenetics and potential influences that anthropogenic and environmental changes have had on structuring the species and populations thereof. Both molecular and morphological data were used as individual datasets and combined in a total evidence approach. Biogeographic inferences were made based on recent detailed Namib biogeography and the ages of the species were estimated using the molecular clock method. A phylogeographic study was done on three of the species of Scarabaeus (Pachysoma) – S. (P.) hippocrates, S. (P.) gariepinus and S. (P.) denticollis - that had previously shown south-north morphological clinal variation. Lastly, an attempt was made to isolate microsatellite loci for Scarabaeus, in the hope of characterising genetic diversity within and between populations of the same species. Scarabaeus (Pachysoma) was found to be monophyletic within Scarabaeus and was therefore classified as a derived subgenus thereof. Morphologically Scarabaeus (Pachysoma) was shown to have 13 species while at a molecular level strong resolution for 11 of the 13 was obtained. S. (P.) hippocrates and S. (P.) glentoni formed a species complex the hippocrates/glentoni complex. The combined phylogenetic tree showed good overall support for all 13 species. Both the morphological and molecular data partition phylogenies show congruence with the combined phylogeny, lending support for combining datasets. Scarabaeus (Pachysoma) appears to have arisen 2.9 million years ago. The formation of advective fog is a consistent water source for Desert dwelling organisms and appears to be associated with Scarabaeus (Pachysoma) radiation into inhospitable areas. Analysis of gene flow revealed large amounts of south-north movement, lending support for movement of psammophilous taxa with their substratum, the barchan dune. Population demographics of the three species, S. (P.) hippocrates, S. (P.) gariepinus and S. (P.) denticollis, chosen for this study differed greatly except in areas of geographic similarity. Major rivers appear to have acted as gene barriers, allowing for distinct genetic entities to be identified within the three species. Phylogeographic partitioning was supported by an AMOVA analysis. All three species were shown to have undergone historical population expansion dating back to the Pleistocene era. Nested Clade Analysis indicated that allopatric speciation; isolation by distance and continuous range expansion could be the factors having affected overall population structure. Recent events show that human induced factors, environmental barriers and reduced vagility have influenced the species population structure. Four potentially polymorphic loci were isolated for Scarabaeus using the FIASCO protocol. Identification of at least one additional locus is needed in order to obtain statistical significance for future studies directed at uncovering recent population dynamics. / Thesis (PhD (Entomology))--University of Pretoria, 2007. / Zoology and Entomology / unrestricted

Indiana University-Purdue University Indianapolis (IUPUI) / Non-rainfall waters such as fog and dew are considered as important source of water in drylands, and the knowledge of possible sources of its formation is very important to make future predictions. Prior studies have suggested the presence of radiation fog in drylands; however, its formation mechanism still remains unclear. There have been earlier studies on the effects of fog on soil moisture dynamics and groundwater recharge. On the contrary, no research has yet been conducted to understand the contribution of soil moisture and groundwater to fog formation. This study, therefore, for the first time intends to examine such possibility in a fog-dominated dryland ecosystem, the Namib Desert. The study was conducted at three sites representing two different land forms (sand dunes and gravel plains) in the Namib Desert. This thesis is divided into two parts: the first part examines evidences of fog formation through water vapor movement using field observations, and the second part simulates water vapor transport using HYDRUS-1D model. In the first part of the study, soil moisture, soil temperature and air temperature data were analyzed, and the relationships between these variables were taken as one of the key indicators for the linkage between soil water and fog formation. The analysis showed that increase in soil moisture generally corresponds to similar increase in air or soil temperature near the soil surface, which implied that variation in soil moisture might be the result of water vapor movement (evaporated soil moisture or groundwater) from lower depths to the soil surface. In the second part of the study, surface fluxes of water vapor were simulated using the HYDRUS-1D model to explore whether the available surface flux was sufficient to support fog formation. The actual surface flux and cumulative evaporation obtained from the model showed positive surface fluxes of water vapor. Based on the field observations and the HYDRUS-1D model results, it can be concluded that water vapor from soil layers and groundwater is transported through the vadose zone to the surface and this water vapor likely contributes to the formation of non-rainfall waters in fog-dominated drylands, like the Namib Desert.

Specific questions regarding the community structure of VAmycorrhizal fungi and the population biology of an ectomycorrhizal addressed. The Basidiomycete, distributional Suillus granulatus, were ecology of VAM fungal communities with grasses was studied across a climatic gradient in the hyper-arid central Namib dune field. VAM fungal communities were primarily structured by substrate stability and moisture availability. Five VAM species were found throughout the study area and were not host specific. Percent mycorrhizal colonization was correlated with moisture availability, whereas spore abundance was correlated with substrate stability. Moisture availability was the key factor influencing VAM fungal phenology: growth, assessed as increased colonization of roots, continued as long as moisture was available, and spore production occurred in response to declining moisture availability. While abiotic factors determine community structure of VAM fungi in the Namib dune field, preliminary studies suggest that the phytobiont mediates fungal response to these abiotic factors. Genetic analyses of S. granulatus single spore isolates using RAPD markers showed that a post-meiotic mitosis in the basidium produces heterokaryotic spores. Secondary homothallism provides an effective means for long distance dispersal, and may account for the broad geographic range of this ectomycorrhizal fungus. Secondary homothallism contributed to the failure of somatic incompatibility tests to delineate the spatial distribution of individuals in a natural population of s. granulatus. Analysis of genetic relatedness using RAPD markers demonstrated conclusively that somatically compatible individuals were not necessarily genetically identical. I concluded that RAPD marker analysis provides a more effective means for determining clonal distribution in ectomycorrhizal populations, than does somatic incompatibility testing. / Ph. D.

Thesis (MScEng)--Stellenbosch University, 2010. / ENGLISH ABSTRACT: This project originated when a team of scientists at the Gobabeb training and research and centre observed seed accumulation sites on the slope of sand dunes in the Namib Desert. Seeds that accumulate on the slip face of a sand dune provide food for small desert creatures that in turn attract larger animals, resulting in a small ecosystem on the side of the dune. Since wind is the primary transport of seeds throughout the Namib Desert it is of interest to investigate wind patterns over the dune. In this project it is therefore desired to look at seed dynamics and deposition as a result of near surface wind patterns around a three-dimensional dune geometry using computational fluid dynamics. The project is a joint venture between the University of Stellenbosch and the University of Namibia. This document presents the South African MScEng thesis part. The literature review shows the dominant winds in the Namib Desert to be from the south to westerly direction. Previous studies on air flow over dunes focussed on sand movement and were often limited to simplified two-dimensional geometries and steady state simulations. From these studies the basic flow features associated with dunes can be identified. Lastly, factors that influence particle dynamics around dune geometries are looked at. These particle studies mostly involve the movement of sand rather than seeds but still provide valuable insight. The project methodology is explained and includes the equipment used, the considerations taken into account, the simplifications made as well as the procedure followed when conducting field work and simulations. A section of an actual Namibian linear dune is mapped in order to obtain a geometry for the simulations. Flow measurements are carried out with a wind mast to obtain velocity profile inlet conditions for the simulations. Furthermore, seed sampling is done by the collaborating Namibian team of which the data is used to obtain an effective seed particle model. Lastly, simulations are carried out using primarily OpenFOAM-1.5. The simulations look at general near surface wind patterns, time dependant flow features and particle movement and seed deposition around and on the linear dune. The results show different wind profiles for different wind direction. It is also possible to see how the profile changes as the flow accelerates up the dune slope. Two-dimensional results provide the opportunity to compare results with previous studies as well as to provide the basis for looking at aspects such as differencing schemes, turbulence models and parallel computing before three-dimensional simulations are carried out. The importance of higher order differencing schemes are confirmed in the two-dimensional results. The turbulence models, however, produce very similar results. The results from the two- and three-dimensional results show typical flow features associated with dunes. Transient flow features and separation vortex structures can be identified from time dependant simulations. Furthermore, particle simulations reveal how particles tend to be trapped in the recirculation regions. The conclusions explain how the project objectives were achieved and provide recommendations for future studies related to this project. / AFRIKAANSE OPSOMMING: Die projek het ontstaan toe naforsers areas van saad akumulasie op die hellings van duine in Namibë opgelet het. Hierdie akumulasie van plant materiaal verskaf die voedsel vir klein diere op die duin wat ‘n klein ekosisteem tot gevolg het. Aaangesien die primêre vervoermiddel vir sade in die woestyn wind is beoog die projek om deur die wind patrone oor die duin beter te verstaan die saad verspreiding te beskryf. Die doel is dus om saad verspreiding en akumulasie te beskryf deur die wind patrone te bekyk wat die verspreiding tot gevolg het deur gebruik te maak van numeriese vloei dinamika. Die projek is ‘n saamgestelde projek tussen die Universiteit van Stellenbosch en die Universiteit van Namibië. Hierdie dokument behels die Suid Afrikaanse MScIng gedeelte van die projek. Deur die hersiening van literatuur word daar gesien dat die domineerende wind rigtings as suid tot wes beskryf kan word. Vorige studies wat verband hou met wind vloei oor duine wys dat die meeste op twee-dimensionele eenvoudige geometrië gefokus het met tyd onafhankike simulasies. Dit is egter moontlik om die resultate te gebruik om karakteristieke vloei patrone te identifiseer wat met duin wind patrone geassosieer kan word. Laastens word daar gekyk na die faktore wat partikel beweeging beïnvloed, maar hierdie studies sluit hoofsaaklik sand partikels in eerder as sade. Die motodologie beskryf die toerusting, oorwegings en prosedures wat gevolg is tydens veld werk asook simulasies. Tydens die veld werk is ‘n gedeelte van ‘n Namib lineêre duin gemeet en so gebruik om ‘n geometrie te maak wat vir simulasie doeleindes gebruik kan word. Daar is ook wind meetings gedoen met ‘n wind mas om wind profiele vir inlaat kondisies vir die simulasies te kry. Verder het saad bestudeering die nodige data verskaf om ‘n voledige saad partikel model op te stel wat in die simulasies gebruik kan word. Laastens kyk die simulasies veral na algemene vloei patrone, tyd afhanklike vloei effekte en ook partikel beweging in die vloei veld. Die resultate wys hoe wind profiele verskil wat van verskillende rigtings af waai. Dit is ook moontlik on te wys hoe die wind profiele verander soos die wind versnel teen die duin op. Tweedimensionele simulasies verskaf die geleentheid om te kyk na die effek van verkillende numeriese modelle, turbulensie modelle en ook multi-prosesseerder verwerking. Tydens die twee-dimensionele simulasies is die belangrikheid van hoër orde numeriese metodes besef. Die verkillende turbulensie modelle het egter klein verkille gewys. Alby die twee- en driedimensionele resultate wys karakteristieke vloei patrone wat met duine geasosieer kan word. Verder het tyd afhanklike simulasies gewys hoe wind patrone verander met tyd. Die partikel simulasies wys ook die beweging van partikels deur die wind en hoe dit neig om te akumuleer in die hersirkulasie gebied agter die duin. Die gevolgtrekkings wys dat al die doelstellings bereik is en maak voorstelle vir toekomstige studies wat met hierdie studie verband hou.

The main aim of this study was to investigate the effects of water availability and SO2 pollution, imposed separately or simultaneously, on the photosynthetic metabolism of Augea capensis Thunb., a succulent of the Namib Desert in the region of Skorpion Zinc mine, Namibia. The main driver for this investigation was the need to distinguish between the effects of water availability on plants native to a desert environment, where water availability dominates plant response, but where the possibility of anthropogenic SO2 pollution poses a new threat to the unique succulent vegetation. Fifteen measuring sites were selected in the vicinity of the mine to determine how rainfall influenced the physiological status of the vegetation. Chlorophyll a fluorescence measurements, and analysis of recorded OJlP fluorescence transients with the JIP-test, were used for this purpose. A series of laboratory experiments were also conducted on A. capensis to determine the precise physiological response that water deprivation and SO2 pollution had under controlled growth conditions. Potted plants were exposed to water deprivation or SO2 fumigation in the light or dark. Besides chlorophyll a fluorescence, photosynthetic gas exchange and Rubisco activity were also measured. Changes in fast fluorescence rise kinetics observed under field conditions suggest considerable modulation of photosystem II function by rainfall with concomitant involvement of a heat stress component as well. In both the field and laboratory experiments, one of the JIP-test parameters, the so-called performance index (PIABS), was identified as a very sensitive indicator of the physiological status of the test plants. Moreover, under laboratory conditions, a good correlation existed between the water deprivation-induced decline in CO2 assimilation rates and the decline in PIABS values. The JIP-test in general, and the PIABS in particular, shows considerable potential for application in the investigation of water availability influences on desert ecosystems. In the laboratory experiments, water deprivation caused stomatal closure but also a slight elevation in intercellular C02 concentration and inhibition of Rubisco activity, suggesting that mesophyll limitation was the dominant factor contributing to the decrease in C02 assimilation rates. Following re-watering, A. capensis showed remarkable recovery capacity. Fumigation of A. capensis with 1.2 ppm SO2 in the dark or light revealed relatively small effects on C02 assimilation. The inhibitory effects on photosynthesis were also fully reversible, indicating no permanent metabolic/structural damage. The effects on photosynthesis were more pronounced when fumigation occurred in the dark. This phenomenon might be related to diurnal differences in cellular capacity for SO2 detoxification. When long-term moderate water deprivation was combined with simultaneous SO2 fumigation, there was no additional inhibitory effect on photosynthesis. These findings suggest that water deprivation do not increase sensitivity towards SO2 pollution in A. capensis. Fumigation with SO2, singly or in combination with water deprivation also had no major effect on chloroplast ultrastructure. It appears that A. capensis is remarkably resistant to SO2 pollution even in the presence of low water availability, which is a common phenomenon in desert ecosystems. Since A, capensis seems to be highly tolerant to S02, its suitability as an indicator species for the detection of SO2 pollution effects at Skorpion Zinc mine is questionable. Because water availability dominates the physiological/biochemical response in this species, subtle SO2 pollution effects might be difficult to detect against this dominant background. The high water content of A. capensis and similar succulents might act as a substantial sink for SO2 and could convey considerable tolerance against this form of air pollution. / Thesis (M.Sc. (Botany))--North-West University, Potchefstroom Campus, 2006.

Cette thèse présente les données des pollens et micro-charbons fossiles couvrant la période des 50 000 dernières années à partir de sites sélectionnés transversalement nord-sud du désert de Namib. Dans le cadre de cette thèse, on utilise le rock hyrax middens, l’accumulation des boulettes et des urines fossilisés du Procavia capensis, représentant une excellente archive pour archives pour la préservation des pollens et micro-charbons à long-terme. Trois sites des hyrax middens ont été sélectionnés pour l'analyse: au sud du désert de Namib (Pella), la marge est des dunes de sable de Namib (Zizou) et le centre de la Namib (Spitzkoppe). En plus, le régime pluvial de ces sites se caractérise par une forte variabilité annuelle et interannuelle. En conséquence, tous ces sites se situent au long de l’écotone du Désert et du biome Nama-Karoo, ainsi qu'à l’est (biome de Savane). Alors que ces sites sont répertoriés dans des écosystèmes similaires, l’écotone, lui, est considéré comme une zone potentiellement très sensible au changement du système climatique régional. Un intérêt spécifique de ces enregistrements terrestres est pour évaluer s’ils corroborent ou s’opposent avec les résultats provenant ceux des sédiments marins de la côte namibienne, en particulier la conclusion : l’abondance des taxa dominants du Fynbos Biome du Cape peut indiquer significativement une expansion vers le nord de la flore du Cape pendant les périodes plus froides glaciaires. Selon les sites d’études sélectionnées, les conclusions principales de ce travail sont les suivantes:Les hyrax middens de Pella fournissent le premier enregistrement pollinique continué au sud du désert de Namib durant la période des 50 000 dernières années. Ces données polliniques ont permis de reconstruire le changement de la végétation et d'estimer la température et l'aridité. Les résultats indiquent que la période glaciaire se caractérise par une augmentation de la disponibilité de l'eau sur le site par rapport à l'Holocène. Les changements de la température et de l'évapotranspiration potentielle semblent avoir joué un rôle important dans la détermination de l'équilibre hydrologique.L'enregistrement de Zizou hyrax midden met en évidence des changements de la végétation à la marge l'est des dunes de sable depuis 38 000 ans cal BP. La végétation de la période glaciaire se caractérise par les pourcentages relativement élevés des Astéracées pollen, et plus particulièrement par des taxa du climat plus froid: Stoebe et Artemisia¬-type. En accord avec les données de Pella, le réchauffement au début de l'Holocène indiqué par la dominance de pollen des graminées dans l'assemblage pollinique suggère une expansion du biome de Désert.Les hyrax middens de Spitzkoppe enregistrent les changements de la végétation dans le centre du désert de Namib au cours des 32 000 dernières années. Les résultats sont globalement cohérents en comparant aux autres enregistrements terrestres dans la région. L'analyse de ces données n'est cependant pas encore terminée.Dans tous ces sites, une variabilité significative a été observée à la fois dans la dernière période glaciaire et l'Holocène. Les conditions plus froides de l'ère glaciaire semblent être caractérisées par une augmentation de la disponibilité de l'eau le long de la totalité de notre zone d'étude. Au contraire des résultats provenant des carottes marines, nos enregistrements indiquent aucune expansion de la végétation de Fynbos biome, et seulement des traces de Restionaceae pollen dans le site extrêmement au sud à Pella (pas plus de 1%), mais aucun trace de ce pollen n'ayant été observé à Zizou ainsi qu’à Spitzkoppe. / This thesis presents fossil pollen and microcharcoal data during the last 50,000 years from a north-south transect of the Namib Desert. The arid environment of the Namib precludes the development of permanent wetlands, and as a result few palaeoenvironmental records exist from the region. In this study, we employ rock hyrax middens – fossilised accumulations of the faecal pellets and urine of the Procavia capensis. Hyrax middens from three sites were selected for analysis: the southern Namib (Pella), the eastern margin of Namib Sand Sea (Zizou), and the central Namib (Spitzkoppe). The results from these terrestrial sites are the extent to which they may corroborate or conflict with findings from pollen records obtained from marine sediments of the Namibian coast.The Pella hyrax middens provide the first continuous pollen record from the southern Namib Desert since the last 50,000 years, and are used to reconstruct vegetation change and quantitative estimates of temperature and aridity. Results indicate that the last glacial period was characterised by increased water availability relative to the Holocene. Changes in temperature and potential evapotranspiration appear to have played a significant role in determining the hydrologic balance. The record can be considered in two sections: 1) the last glacial period, when low temperatures favoured the development of more mesic Nama-Karoo vegetation at the site, with periods of increased humidity concurrent with increased coastal upwelling, both responding to lower global/regional temperatures; and 2) the Holocene, high temperatures and potential evapotranspiration resulted in increased aridity and an expansion of the Desert Biome.Considered in the context of discussions of forcing mechanisms of regional climate change and environmental dynamics, the results from Pella stand in clear contrast with many inferences of terrestrial environmental change derived from regional marine records. Observations of a strong precessional signal and interpretations of increased humidity during phases of high local summer insolation in the marine records are not consistent with the data from Pella. Similarly, while high percentages of Restionaceae pollen has been observed in marine sediments during the last glacial period, they do not exceed 1% of the assemblage from Pella, indicating that no significant expansion of the Fynbos Biome has occurred during the last 50,000 years.The Zizou hyrax midden highlights vegetation changes on the eastern margin of the Namib Sand Sea since 38,000 cal BP. Results show the different vegetation compositions between the last glacial period and the Holocene. Glacial vegetation characterised with relatively high percentages of Asteraceae pollen, particularly cool climate taxa such as Stoebe and Artemisia types. Similar to the data from Pella, with the onset of Holocene warming grass pollen comes to dominate the assemblage, suggesting an expansion of the Desert Biome. We suggest that the climate during the last glacial period was more humid, and supported the development of shrubs/small trees. Arid conditions during the Holocene saw the depletion of this resource, and the development of grasslands that could exploit the rare rains that the region experiences today. In common with the Pella record, no elements of the Cape flora are found in the Zizou middens.The Spitzkoppe hyrax middens record vegetation changes in the central Namib during the last 32,000 years. The last glacial vegetation compositions composed of Olea, Artemisia¬-type, Stoebe¬-type and grasses. In the Holocene, the arboreal taxa such as Olea was replaced by others like Eculea, Dombeya, Commiphora, and Croton¬-type with relative higher percentage of grasses at early Holocene.

The main aim of this study was to investigate the effects of water availability and SO2 pollution, imposed separately or simultaneously, on the photosynthetic metabolism of Augea capensis Thunb., a succulent of the Namib Desert in the region of Skorpion Zinc mine, Namibia. The main driver for this investigation was the need to distinguish between the effects of water availability on plants native to a desert environment, where water availability dominates plant response, but where the possibility of anthropogenic SO2 pollution poses a new threat to the unique succulent vegetation. Fifteen measuring sites were selected in the vicinity of the mine to determine how rainfall influenced the physiological status of the vegetation. Chlorophyll a fluorescence measurements, and analysis of recorded OJlP fluorescence transients with the JIP-test, were used for this purpose. A series of laboratory experiments were also conducted on A. capensis to determine the precise physiological response that water deprivation and SO2 pollution had under controlled growth conditions. Potted plants were exposed to water deprivation or SO2 fumigation in the light or dark. Besides chlorophyll a fluorescence, photosynthetic gas exchange and Rubisco activity were also measured. Changes in fast fluorescence rise kinetics observed under field conditions suggest considerable modulation of photosystem II function by rainfall with concomitant involvement of a heat stress component as well. In both the field and laboratory experiments, one of the JIP-test parameters, the so-called performance index (PIABS), was identified as a very sensitive indicator of the physiological status of the test plants. Moreover, under laboratory conditions, a good correlation existed between the water deprivation-induced decline in CO2 assimilation rates and the decline in PIABS values. The JIP-test in general, and the PIABS in particular, shows considerable potential for application in the investigation of water availability influences on desert ecosystems. In the laboratory experiments, water deprivation caused stomatal closure but also a slight elevation in intercellular C02 concentration and inhibition of Rubisco activity, suggesting that mesophyll limitation was the dominant factor contributing to the decrease in C02 assimilation rates. Following re-watering, A. capensis showed remarkable recovery capacity. Fumigation of A. capensis with 1.2 ppm SO2 in the dark or light revealed relatively small effects on C02 assimilation. The inhibitory effects on photosynthesis were also fully reversible, indicating no permanent metabolic/structural damage. The effects on photosynthesis were more pronounced when fumigation occurred in the dark. This phenomenon might be related to diurnal differences in cellular capacity for SO2 detoxification. When long-term moderate water deprivation was combined with simultaneous SO2 fumigation, there was no additional inhibitory effect on photosynthesis. These findings suggest that water deprivation do not increase sensitivity towards SO2 pollution in A. capensis. Fumigation with SO2, singly or in combination with water deprivation also had no major effect on chloroplast ultrastructure. It appears that A. capensis is remarkably resistant to SO2 pollution even in the presence of low water availability, which is a common phenomenon in desert ecosystems. Since A, capensis seems to be highly tolerant to S02, its suitability as an indicator species for the detection of SO2 pollution effects at Skorpion Zinc mine is questionable. Because water availability dominates the physiological/biochemical response in this species, subtle SO2 pollution effects might be difficult to detect against this dominant background. The high water content of A. capensis and similar succulents might act as a substantial sink for SO2 and could convey considerable tolerance against this form of air pollution. / Thesis (M.Sc. (Botany))--North-West University, Potchefstroom Campus, 2006.