African rock rats of the genera Aethomys Thomas, 1915 and Micaelamys Ellerman, 1941, are endemic to East, Central and southern Africa but extend marginally into West Africa. In the past 16 subspecies have been described in the Namaqua rock mouse M. namaquensis Smith, 1834. Recent morphometric and morphological patterns of intraspecific variation suggested the recognition of only four subspecies: M. n. namaquensis, M. n. alborarius, M. n. monticularis and M. n. lehocla, of which the distributions appeared to coincide with the major phytogeographical zones of southern Africa. In the present study earlier analyses of mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene variation were extended. Taken together these results show that M. namaquensis represents a polytypic species complex but with much more diversity than detected using morphology. Phylogenetic and phylogeographic analyses revealed 14 genetically distinct lineages of which several show strong geographic association with particular vegetation biomes or bioregions. The distributional ranges of eight of these lineages showed some correspondence with the type localities of previously described subspecies of M. namaquensis. Some clades displayed considerable within-lineage variation indicating possible fine-scale population structuring, while others showed very little differentiation. Divergence times between lineages varied between 7.26 MYA and 2.70 MYA, corresponding to a Late Miocene to Pliocene radiation. Cytochrome b sequences alone do not fully resolve the evolutionary relationships among the lineages and the phylogenetic analysis was thus supplemented with nuclear Recombination Activating Gene 1 (RAG1) sequences. This gene was successfully sequenced for 11 of the identified lineages. Independent analyses of the two genes were not congruent possibly as a result of incomplete lineage sorting of the nuclear gene. The combined dataset yielded good support for six of the lineages. Finally, a more detailed phylogeographic analysis was conducted among ten localities of the Eastern Kalahari Bushveld lineage based on mitochondrial cyt b sequences to elucidate processes underlying diversification in this species complex. A genetic pattern of phylogenetic continuity with a lack of spatial separation was observed. The mismatch distribution analysis suggests that the lineage has expanded its population size and the geographical expansion may have followed environmental changes in the recent past. Estimates of female gene flow indicate connectivity among localities but not to the extent expected for a panmictic population. Instead a combination of a stepping-stone model and metapopulation dynamics may be applicable to this lineage. Examination of type material of described subspecies is needed to resolve the identity of the unique lineages which will allow us to better understand the phylogeography and mode of speciation in M. namaquensis. In addition, localities of sympatry (lineages in sympatry) should also be studied in more detail in order to help resolve the current taxonomic uncertainties within M. namaquensis. Future research should therefore include a multidisciplinary approach, such as cytogenetics, morphology and more gene regions. Copyright / Thesis (PhD)--University of Pretoria, 2010. / Genetics / unrestricted

M.Sc. (Geology) / The Proterozoic Namaqua-Natal Mobile Belt of southern Africa represents a succession of high grade metamorphosed igneous and sedimentary rocks rimming the southern and western extents of the Kaapvaal craton. Different petrological processes associated with the onset of granulite facies metamorphism were investigated with the emphasis on the processes on anatexis and migmatitization and the influence of the fluid phase on these processes. The investigation took place in the Margate Terrane of the Southern Natal Metamorphic Province. The Umzimkulu and Louisiana Quarries near Port Shepstone formed the bulk of the field area for this investigation. The Umzimkulu and Louisiana quarries expose two s-type granitic lithologies, namely, the Glenmore Biotite Gneiss (GBGn) and the slightly younger, intrusive Margate Leucogranite (MLGn), both of which have been metamorphosed to granulite facies. Geothermobarometric calculations on the metamorphism of the Margate Terrane all indicate temperatures and pressures of peak metamorphism be 850oC+50oC at +6 kbar. The high grade metamorphic history of the lithologies is recorded by the formation of concordant, lens-shaped, prograde anatectic leucosomes. The leucosomes are concentrically surrounded by biotite selvage zones, followed by melanosomes, and lastly undisturbed host rock material. This investigation revealed that the formation of both the charnockite veins and the prograde leucosomes occurred through processes of anatexis. Field relations suggest that the charnockitic veins formed in situ, and were structurally controlled, which is evident from their linearity. Petrographic and geochemical data provide evidence for melt involvement. This is in strong contrast to theories of charnockite formation ascribed to subsolidus granulite formation by the flushing of host lithologies by a pervasive, carbonic fluid, as has been suggested to have occurred in Southern India. The so-called "incipient charnockites" of Southern India are both morphologically and geochemically similar to the charnockite veins described in the SNMP, suggesting that an anatectic origin may be common to both.

Genetic and phenotypic characterisation is essential for the conservation and utilisation of farm animal genetic resources, especially indigenous types that are often disregarded due to lower production potential compared to commercial breeds. In this study a genetic characterisation was performed on 144 Namaqua Afrikaner sheep kept at the Karakul Experimental Station (KES) and Carnarvon Experimental Station (CES) and a private farm Welgeluk (WGK) using 22 ISAG recommended microsatellite markers. Results of this study showed that the mean number of alleles were low (3.6 for KES to 4.2 for WGK) for the loci tested. Heterozygosity values across loci ranged between 46% for WGK, 48% for KES and 55% for CES, indicating low to moderate genetic variation within the different populations. The AMOVA analyses revealed that 89.5% of the genetic variation in the breed was due to the differences within populations and 10.5% due to differences between populations. The genetic distance estimates revealed a close relationship between the CES and WGK populations. The population structure confirmed the differentiation of three clusters with relationships between the CES and WGK populations. Phenotypic characterisation of the breed was limited to the Carnarvon flock, where production and morphological data were recorded. Morphological measurements indicated an average body length of 71.2 cm and 68.7 cm for rams and ewes respectively. Over 60% of the sheep had their tail twisted to the left. The molecular data provided by this study will serve as a reference for genetic management and breeding strategies of the indigenous Namaqua Afrikaner sheep. Copyright / Dissertation (MSc(Agric))--University of Pretoria, 2011. / Animal and Wildlife Sciences / unrestricted

>Magister Scientiae - MSc / The Proterozoic Namaqua-Natal Province comprises highly deformed rocks of medium to high grade metamorphism and is bordering the Archean Kaapvaal Craton to the west, south and east in South Africa. The sector to the west of the Craton, namely the Namaqua Sector, is structurally complex and subdivided from west to east into the Bushmanland Subprovince, the Kakamas and Areachap terranes of the Gordonia Subprovince and the Kheis Subprovince. The prominent Neusberg Mountain Range, with exposures to the north and south of the Orange River in the Kakamas Terrane constitutes evidence of crustal shortening as a result of continental collision of the Namaqua Sector block with the Kaapvaal Craton during the Namaquan Orogeny. The Mesoproterozoic Korannaland Group in the Kakamas Terrane is affected by faulting, folding and shearing.

Thesis (MSc)--University of Stellenbosch, 2006. / Bibliography. Also available via the Internet.

>Magister Scientiae - MSc / The group of granites on the eastern margin of the Mesoproterozoic Namaqua sector of the polydeformed and highly metamorphosed Namaqua-Natal Province of southern Africa is known as the Keimoes Suite. The suite includes mixtures of diverse rock types not belonging to a single intrusive series and so it should be subdivided into more than one intrusive suite. The exact definition, extent, distribution and petrogenesis of these granites have been poorly defined in the past, with various authors defining the suite differently due to the lack of proper geochronology and geochemical data. The exact contact between the Namaqua sector and Kaapvaal Craton together with the role of the suite to the Namaqua tectonic evolution is still unclear. The granites of the Keimoes Suite are thought to mark the contact between the Namaqua sector and the Kaapvaal Craton. This study seeks to address the above mentioned problems by making use of new geochronology, isotope, major and trace element geochemistry together with petrography. The granites of the Keimoes Suite were previously grouped based on their degree of deformation. The geochronology, undertaken as part of this study, has proven that this classification is unfounded. The degree of foliation in these granites appears to be largely controlled by the abundance of platy minerals, such as biotite and muscovite, together with the intrusion mechanism, with deformational processes, such as shearing, playing a secondary role. The geochronology, together with geochemistry has helped to redefine the previously defined Keimoes Suite so that two well defined separate suites are recognized and the third is poorly defined due to lack of more samples of that age group. The new classification or grouping of the granites of the eastern Namaqua sector allows a more detailed examination of the tectonic evolution of this region. A member of the 1225 to 1200 Ma early syn-tectonic granites, the Josling Granite, shows a strongly developed foliation and was derived from a depleted source with a relatively low continental crustal component. This granite intruded during the time of arc accretion, and is associated with, and partly responsible for the D₁ deformation and M₁ metamorphism recognized in most of the rocks of the eastern terranes of the Namaqua sector. In terms of age, the syn-tectonic granites of the Augrabies Suite extend from 1200 to 1120 Ma and were largely derived from depleted sources with variable but more substantial amounts of continental crustal components as compared to the early syn-tectonic granite. The granites of this suite intruded during the period of peak D₂ deformation with peak magmatism between 1180 - 1135 Ma, and particularly around 1150 Ma, during the peak of metamorphism (M₂) caused by, and associated with these voluminous intrusions. The Keimoes Suite can now be defined as comprising granites of late- to post-tectonic age relative to the 1.2 - 1.08 Ga Namaquan Orogeny with magmatism occurring on the western side of the Kaapvaal Craton. The 1116 to 1066 Ma Keimoes Suite intruded during the stage of the Namaquan Orogeny in which there was continued indentation of the Kaapvaal Craton into the Namaqua sector with wrenching and shearing causing the development of rifting into which the granites intruded. The Keimoes Suite granites were derived from continental crustal sources and incorporated varying degrees of depleted source components. The intrusives and extrusives of this age occured after the main collisional event between the Namaqua Sector and the Kaapvaal Craton and are associated with the D₃ deformational event, imparting the thermal conditions leading to the M₃ metamorphic event of the rocks within both the Kakamas and Areachap Terranes. The suites mark the suture between the Archean Kaapvaal Craton and the Proterozoic Namaqua sector. The compositions of the granites of the individual suites were mainly controlled by the source with the degree of partial melting exerting a major control. The proportion of entrained peritectic assemblages and accessory minerals played a major role in controlling the compositions of the granites, particularly those of the trace elements. Variations within the compositions of the same suite are due to source heterogeneities. Generally, fractionation processes played a secondary role in influencing the composition of the granites. / Council for Geoscience and National Research Foundation

>Magister Scientiae - MSc / The Keimoes Suite is a group of poorly defined granitoids that characterize the Namaqua Front and Foreland zones. There is a lack of knowledge on its content and distribution. A significant amount of work has been done on the geochemical and geochronological aspects of the Keimoes Suite but no structural analysis using a comparison between joint occurrences in the suite and the country rock has been found in the literature. This study provides insight on whether these joints formed as a result of the emplacement and subsequent cooling of the granitoids or whether they are the result of later deformation processes. This was achieved through remote sensing, detailed field mapping and structural analysis of joint data to determine the type of stress regime associated with their deformation. Eleven granitoids of the Keimoes Suite were mapped in the Kakamas-Keimoes area in the Northern Cape, South Africa. Up to four joint sets were mapped and characterized according to orientation, abutting relationship, in-filling material and spacing properties. The orientation analysis revealed two prominent joint sets (NNW and NE) that are consistent throughout the Keimoes Suite granite. However after careful analysis of their abutting relationship it has been concluded that these joints are the youngest joints formed in the Keimoes Suite. The fourth set is the E-W set which does not occur at a wide spread scale. The oldest joint set (NNE) is defined by the quartz and feldspar filling and these joints only occur in the oldest granite of the suite. Field observation revealed shear displacement, forming a conjugate joint set. This conjugate set closes at an acute angle of 60˚ and the joints displace each other. The presence of en echelon sigmoidal veins suggests these joints formed as mode II fractures and that they are tectonic joints. The dominant joint set NNW is parallel to the regional foliation, shear zones and faults which were formed during the D2 deformational vent of the Namaqua Orogeny. This NNW joint set post-dates the D2 deformational event and was formed during the D3 deformational environment of the Namaqua Orogeny. Principal stress analysis of all the joints in the study area suggests a strike-slip environment, which coincides with the D3 deformation event of the Namaqua Natal Province. Even though the country rock and the Keimoes Suite granites were subjected to same stress field during the D3 event, the analysis of principal stresses between the Keimoes Suite granites and the country rock reveals a slight difference in the orientation of the principal stresses. This is caused by the difference in competency between the Keimoes Suite granites and the country rock thus caused the refraction. In conclusion Structural evidence on various members of the Keimoes Suite indicates three episodes of intrusions with respect to the D2 Namaqua deformation event based on foliation and mineral filled joints. The Vaalputs Granite is pre tectonic relative to the main D2 deformation event and the thermal peak M2 metamorphisms, while Louisvale, Kanon Eiland and Klip Kraal Granites are syn-tectonic to these deformation events. The granites that lack foliation are classified as post-tectonic granites and these are the Keboes, Kleinbegin, Gemsbokbult, Colstone and Cnydas Granites as well as the Friesdale Charnockite. However the presence of foliation in some granites suggests that a compressional episode existed for a period of time and ended sometime before the onset of the post-tectonic granites. Therefore the D2 pre-dates the last episode of Keimoes Suite granite emplacement. This study partly validates the work done by previous workers on the Keimoes Suite, although there are some slight differences which are subjected to change. Conclusion can be drawn that this study provided additional insight in the findings of other workers nonetheless also differs with some of their findings regarding the timing of emplacement of the Keimoes Suite.

The genlogy of the Namaqua Province is notoriously difficult to map and interpret due to polymetamorphic and multiple deformation events and limlted outcrop. Current maps of the Province reflect diverse interpretations of stratigraphy as a consequence of these difficulties. A Geographic Information System is essentially a digital database and a set of functions and procedures to capture, analyse and manipulate spatially related data. A GIS is therefore ideally suited to the study and analysis of maps. A digital map database was established, using modem GIS technology, to facilitate the collation of existing maps of an area in the Central Namaqua Province (CNP). This database is based on a lithological classification system similar to that used by Harris (1992), rather than on an interpretive stratigraphic model. In order to establish the database, existing geological maps were scanned into a GIS, and lines of outcrop and lithological contacts were digitised using a manual line following process, which is one of the functions native to a GIS. Attribute data were then attached to the resultant polygons. The attribute database consists of lithological, textural and mineralogical data, as well as stratigraphical classification data according to the South African Committee for Stratigraphy (SACS), correlative names assigned to units by the Precambrian Research Unit, the Geological Survey of South Africa, the Bushmanland Research group and the University of the Orange Free State. Other attribute data included in the database, are tectonic and absolute age information, and the terrane classification for the area. This database reflects the main objective of the project and also serves as a basis for further expansion of a geological GIS for the CNP. Cartographic and database capabilities of the GIS were employed to produce a collated lithological map of the CNP. A TNTmipsTM Spatial Manipulation Language routine was written to produce a database containing two fields linked to each polygon, one for lithology and one for a correlation probability factor. Correlation factors are calculated in this routine from three variables, namely the prominence a worker attached to a specific lithology within a unit or outcrop, the agreement amongst the various workers on the actual lithology present within an outcrop, and the correspondence between the source of the spatial element (mapped outcrop) and the source of the attribute data attached to it. Outcrops were displayed on the map according to the lithology with the highest correlation factor, providing a unique view of the spatial relationships and distribution patterns of lithological units in the CNP. A second map was produced indicating the correlation factors for lithologies within the CNP. Thematic maps are produced in a GIS by selecting spatial elements according to a set of criteria, usually based on the attribute database, and then displaying the elements as maps. Maps created by this process are known as customised maps, since users of the GIS can customise the selection and display of elements according to their needs. For instance, all outcrops of rock units containing particular lithologies of a given age occurring in a specific terrane can be displayed - either on screen or printed out as a map. The database also makes it possible to plot maps according to different stratigraphic classification systems. Areas where various workers disagree on the stratigraphic classification of units can be isolated, and displayed as separate maps in order to aid in the collation process. The database can assist SACS in identifying areas in the CNP where stratigraphic classification is still lacking or agreements on stratigraphic nomenclature have not yet been attained. More than one database can be attached to the spatial elements in a GIS, and the Namaqua-GIS can therefore be expanded to include geochemical, geophysical, economic, structural and geographical data. Other data on the area, such as more detailed maps, photographs and satellite images can be attached to the lithological map database in the correct spatial relationship. Another advantage of a GIS is the facility to continually update the database(s) as more information becomes available and/or as interpretation of the area is refined.

The massive sulphide deposits at Areachap and Kantienpan Cu-Zn Mine are hosted by a ~1600 Ma old volcano sedimentary succession known as the Areachap Group, in the eastern part of Namaqua Metamorphic Province, South Africa. The deposits were affected by a complex deformation and metamorphic history and represent examples of upper amphibolite to granulite grade metamorphosed volcanic-hosted massive sulphide (VHMS) deposits. The host rocks of both ore deposits are peraluminous-gneisses and the dominant sulphide minerals in the ore zone are pyrite, pyrrhotite sphalerite, and chalcopyrite and trace amounts of galena. Other ore related minerals include barite and anhydrite. The metamorphic minerals in the alteration zones at the Areachap and Kantienpan VHMS deposits are characterized by the presence of plagioclase, almandine and pyrope, enstatite and clinoenstatite, cummingtonite and gedrite, cordierite, sillimanite, and retrograde chlorite and chamosite. Lithogeochemical methods are widely used in exploration geochemistry to identify the primary alteration zones related to VHMS mineralization, as these zones are often exposed, while the massive sulphide ore body itself may be concealed. Especially in areas that were not affected by high grade metamorphism and intensive deformation. Some of these methods include the variation in the relative abundance of major element concentrations throughout the rock successions, mineral chemistry of silicates and spinel minerals near the ore zone, and normative compositions of the rock successions. However, the application of these methods is limited by complex geology in regional metamorphic terranes, such as the Namaqua Metamorphic Province. Therefore, in addition, three of the more advanced lithogeochemical approaches, known as the Isocon method, the Box Plot and Pearce Elemental Ratios, are combined here and adapted for application in such regions. Based on the mineral chemistry, it is evident that plagioclase is more Ca-rich adjacent to the ore zone, pyroxene has the highest relative Mg* ratio (Mg* ratio =100 x cationic ratio of Mg / (Mg + Fe + Ca)), the almandine and pyrope components of garnet are high and the spessartine and grossular components are low. In addition, the Mg-rich variety of mica (phlogopite) is more common near the ore zone and the peraluminous nature of the footwall zone is revealed by the presence of gahnite. Cordierite and retrograde chlorites show the highest Mg#’s (Mg# = Mg/ (Mg + Fe)) in the ore zone. In addition to the above, Pearce Element Ratio analyses of cordierite, pyroxene and garnet may be used to define proximity to sulphide mineralization. Geochemically, the ore zone and alteration zones at Areachap and Kantienpan VHMS ore deposits display a high peraluminous ratio (Al2O3 / (Na2O+K2O+CaO)) confirming the peraluminous nature of these zones as indicated by the mineral chemistry discussed above. The intervals identified in sampled borehole core with low CaO and Na2O and with high MgO and K2O contents represent the alteration zone in the original footwall rocks of the deposit. Isocon studies have shown that the alteration zones at the Areachap and Kantienpan deposits are enriched in Mg, Fe (total), S, Zn, Si, Co and F and depleted in Na, Ca, Sr, Ni, V and La. Elements that behaved relatively immobile include Zr, Ti, P, Mn, Al, Y, and U. The box plot, alteration index versus the chlorite-carbonate-pyrite index, was originally proposed to illustrate the combined effects of hydrothermal and diagenetic alteration and is based on characteristic primary mineral reactions in regions not affected by regional metamorphism. It is demonstrated here that these primary mineral reactions are preserved in a unique set of metamorphic minerals, and that the box plot can be modified for high-grade metamorphic rock types. When samples with very high Mg contents (MgO>>K2O, AI>90% and CCPI>98%) are plotted in the box plot they may be classified as representative of anomalous areas that are highly prospective. Samples with high Mg contents (MgO>K2O, AI>64% and CCPI>93%) may be considered representative of areas that may be classified as of moderate priority in an exploration programme. The findings of the mineral chemical and geochemical investigations of the footwall alteration at the Kantienpan, Areachap and Prieska Cu-Zn ore bodies are used to define various statistical factors. The applicability of these factors in lithogeochemical exploration is demonstrated by calculating the respective factor scores for a regional lithogeochemical data set. It is demonstrated how these factors could be used to identify samples collected from localities that are highly prospective for the discovery of concealed VHMS style mineralization. Based on the statistical analyses of the regional data set, the altered rocks may be distinguished from the metapelitic rocks by their high scores for the alteration factor and low scores for the peraluminous factor. The peraluminous rocks may be separated from the hornblende-gneisses by their high scores for the peraluminous factor, and from the amphibolites by their very low ortho-amphibolite factor scores and high peraluminous factor scores. The variation, of trace elements in the surface calcrete layer that conceals the mineralization in the studied areas, displays the geochemical signature of mineralization, but the concentrations of Cu, Zn and Pb are much lower at and near surface and increase down depth within the profiles. The absolute concentrations and peak to background ratios of the elements of interest at the surface therefore depend on the thickness of the underlying calcrete layer in the area. Two methods, a total analysis (x-ray fluorescence, XRF) and partial extraction (NH4EDTA solution), were applied in to evaluate results, which would be successful and commercially viable in a general exploration programme, using regolith samples. The results of the two methods above were then compared to another patented partial extraction method (mobile metal ion, MMI) on a data set previously reported on by Rossouw (2003). At Kantienpan, where the sand cover is very shallow to absent, dispersion appears to be more related to the secondary redistributions of gossaniferous clasts, than to dispersion of mobile metal ions on the surface of sand particles. The XRF method shows a wider dispersion halo here than methods based on partial extraction. Whereas, at Areachap, where a relatively thick sand (approximately one metre) covers the calcrete layer, partial extraction (based on a NH4EDTA solution extraction) results in a larger, recognizable, dispersion halo than that detected by XRF. The MMI results show a larger span for Zn, followed by NH4EDTA and finally XRF. For Cu, the NH4EDTA method exhibits the largest span followed by XRF and then MMI. The anomalous Cu, Zn and Pb contents extracted by partial extraction methods from the wind blown sand deposits indicate that these elements were derived from the ore minerals related to the massive sulphide deposits. However, Mn and Fe contents analysed by XRF also show high values that could not be only related to derivation from massive sulphide ores. Some of the high concentrations of these elements in the sand cover is ascribed to the weathering of other iron-rich rock forming minerals. / Thesis (PhD (Geology))--University of Pretoria, 2006. / Geology / unrestricted

M.Sc. / The Salt River deposit is a poly-metallic base metal deposit with a Zn-Cu-Pb metal content that occurs southwest of the town of Kakamas within the Northern Cape Province, South Africa. The Salt River deposit occurs within the Geelvloer Formation of the Bushmanland Subprovince of the Proterozoic Namaqua Metamorphic Province (NMP). This study constitutes the first detailed study of the host rock succession to the Salt River deposit, by investigating the lithostratigraphy, petrography geochemistry and geochronology. During the course of the study, various styles of wall-rock alteration were identified and investigated to determine their effect on the host rock succession. A further aim of this study was to classify the Salt River deposit and compare it to neighboring deposits occurring in the NMP. Geochronological studies were undertaken to define the age of mineralization. Detailed logging of exploration diamond drill core combined with petrographic investigation was used to define thirteen distinct lithotypes. The stratigraphy is dominated by felsic grey gneisses and mafic amphibolites, minor calc-silicate rocks, granitic augen gneisses, pegmatites and two lithologies that represent the metamorphosed equivalents of hydrothermally-altered host rock. Lithostratigraphic investigations yielded a rather uniform succession containing four distinct marker beds defined by their common occurrence and ease of correlation across various boreholes.