Dissertations / Theses on the topic 'Fishes – South Africa – Geographical distribution'

The Agulhas Bank supports a speciose fish community, many of which are commercially important. Despite substantial research being conducted on aspects of their biology spatial aspects of their distribution and abundance in relation to environment parameters has been ignored. This study, therefore, addressed aspects related to the distribution and abundance of representative species on the Agulhas Bank within a Geographic Information System (GIS). Four candidate species were chosen due to their importance either in numbers or unit mass to the South African demersal trawl fishery. The species also shared morphological and taxonomic similarities. The candidate species chosen were the two Cape hake species, shallow-water hake Meluccius capensis, and deep-water hake Merluccius paradoxus, and the two pleuronectiform species being Agulhas sole Austroglossus pectoralis and redspotted tonguesole Cynoglossus zanzibarensis. The use of a GIS was appropriate and allowed for hidden spatial patterns be exposed and illustrated visually, while also facilitating the quantification of the relationships between distribution/abundance and certain environmental predictors using statistical methods The Department of Marine and Coastal Management, Cape Town, supplied biological data in the form of length frequency and biomass information from spring (AprillMay) and autumn (September/October) cruises conducted between 1986 and 1993 on the R. V. Africana. The Council for National Geoscience, Cape Town, supplied sediment data for the entire southern African coastline. Initial exploratory data analysis highlighted potential relationships between environmental variables and abundance for each specie's life-history stanzas. Variations in spatial distribution were found to be significantly different between each life-history stanzas within species. Fish density as a function of the additive effects of the various environmental parameters, including temperature, depth and sediment type, was assessed using a Poisson Generalized Additive Model (GAM), while distribution was analysed with a logistic GAM. A predictive logistic model was then created, taking into consideration the importance of the predictor variables for each species, allowing for predictive estimates to be made for each species by inputting environmental information within the study area. The importance of certain environmental variables influencing distribution and abundance were noted. General patterns indicated that sediment was the most important to both the distribution and abundance of the two pleuronectiform species and juvenile life-history stanzas, while the adult gadoids' distribution and abundance appeared to be depth dependent.

The results of a community survey of the rocky intertidal and subtidal reef ichthyofauna of the Tsitsikamma National Park and adjacent areas are presented. An updated species checklist is given, comprising 116 species of 46 families, including a new genus and species of Tripterygiid. Single species are shown to dominate, in terms of numbers, both the cryptic and subtidal components for all the areas sampled down the vertical profile. Species richness, evenness and diversity are found to increase with depth for both the cryptic and suprabenthic components. A community level feeding study shows an increase in trophic specialisation with depth and food availability is found to be an important factor delimiting littoral fish vertical distribution. The nursery function of the Tsitsikamma rocky littoral area is assessed and it is shown that shallow littoral areas as a whole are more important than intertidal pools alone in functioning as nurseries. The results of the study are found to fit into the existing trend of an increase in species richness and diversity, from west to east, along the South African coast. A significant difference is shown between the observed frequencies of species on exploited reefs outside the Park and unexploited reefs inside the Park. The density of the key reef predator Petrus rupestris is shown to be nine times more abundant on deep reef inside the park compared to deep reef outside the park (0.0045 fish/m² and 0.0005 fish/m² respectively) and a paucity of larger individuals of this species on exploited reefs is noted. Marked differences in the relative abundance of other species between exploited and unexploited reefs are evident and it is hypothesised that community disruption has occurred on exploited reefs, either directly or indirectly because of the removal of P. rupestris. These results are discussed in the context of marine reserves as a conservation strategy and a recommendation is made to extend the 5.6km seaward boundary of the Tsitsikamma National Park westwards to include the large concentration of presently exploited rocky reefs between the Blaaukrans river mouth and Natures Valley.

Two and a half years of data were collected from the Great Fish River and estuary using seine nets and gill nets to determine the fish species composition within these regions. The head region of the Great Fish River estuary was found to have a rich fish fauna, with the euryhaline marine fish component totally dominating the catch in all three regions. Gilchristella aesiuaria was the single most common species and several euryhaline marine species were captured in freshwater for the first time. Physical parameters were also measured in an effort to ascertain the possible factors which may affect the distribution and length frequency of the most common species within this area. Salinity was found to be the single most important factor affecting the species composition, and the sampling area was consequently divided into three regions, viz. river (< I ‰), head (1-4 ‰) and estuary (> 4 ‰). In addition, it was determined that river flow rate during the month prior to sampling also had a profound effect on species composition in all three regions. Based on the available evidence it is suggested that for most species this is related to conductivity levels rather than flow per se.

Distribution patterns and levels of genetic diversity in extant taxa are a product of complex palaeogeographic processes and climatic oscillations as well as the species’ intrinsic ecological adaptations. The Cape Floristic Region of South Africa presents a unique system for studying the processes that promote species diversification and distribution patterns. This region has a high degree of endemism of both terrestrial and aquatic biota and is clearly isolated from neighbouring areas by the Cape Fold Mountains and the Great Escarpment. The objective of this study was to firstly examine the ecology of freshwater fishes belonging to the genera Galaxias, Pseudobarbus and Sandelia in the south-western CFR. This was followed by an assessment of the genetic diversity of these taxa. Unique lineages were identified and their distribution was mapped. The work aimed to explore the role of the region’s complex palaeogeographic and climatic history as well as the role of the species’ ecological adaptations in driving lineage diversification and shaping contemporary distribution patterns. The four main components of the study can be summarised as follows: 1. Habitat associations of three widely distributed lineages of Galaxias zebratus Pseudobarbus burchelli and Sandelia capensis were evaluated at multiple localities in minimally disturbed mountain tributaries of the Breede, Duiwenhoks and Goukou River systems. The lineages have distinct habitat associations which were related to differences in their morphological traits. The slender-bodied Galaxias ‘nebula’ and the fusiform-shaped Pseudobarbus ‘Breede’ are capable of exploiting upper reaches with faster water velocity. By contrast, the laterally compressed Sandelia ‘eastern’ is restricted to lower reaches, making this lineage more susceptible to a wide array of impacts. 2. A recently discovered lineage of Galaxias zebratus, (Galaxias ‘nebula’), was found to be capable of tolerating emersion for a prolonged period of time. This is the first time that such capabilities have been documented in an African galaxiid. These adaptations have implications for the interpretation of Galaxias ‘nebula’s wide distribution range. 3. The phylogeography of Galaxias ‘nebula’ across its entire distribution range was investigated using two mitochondrial genes (cytochrome c oxidase subunit I (COI) and cytochrome b (cyt b)). This lineage has a complex evolutionary history that was influenced by both intrinsic and extrinsic factors. Rare events such as episodic drainage connections during Pleistocene and Holocene pluvial periods, possibly augmented by river confluences during periods of lower sea-levels and river capture events seem to be the most credible explanation for the extensive contemporary distribution and the relatively shallow genetic divergence between different river systems. 4. Mitochondrial cyt b sequences were used (i) to assess genetic diversity in G. zebratus, P. burchelli and S. capensis from the south-western CFR and (ii) to determine the roles of intrinsic ecological adaptations and extrinsic landscape and climatic changes in promoting genetic diversification and shaping present day distribution patterns of lineages in the three taxa. Marine incursions during periods of major sea-level transgressions are proposed to have isolated populations in upland refugia, thereby driving allopatric divergence in these species. Subsequent connections of rivers during wetter periods and lower sea-levels are proposed to have facilitated post-speciation dispersal of lineages to attain present day distribution patterns. While detailed morphological studies and further genetic analysis are needed to substantiate the taxonomic status of the newly discovered lineages of Galaxias zebratus, Pseudobarbus burchelli and Sandelia capensis, results of the present study indicate that the south-western CFR represents a previously unrecognised centre of freshwater fish diversity and microendemism in the broader Cape Floristic Region. Accurate identification of lineages and comprehensive mapping of their distribution is a fundamental pre-requisite for ecological studies, assessing conservation status and implementation of appropriate conservation measures.

Models that are used for predicting species' potential distributions are important tools that have found applications in a number of areas of applied ecology. The majority of these models can be classified as correlative, as they rely on strong, often indirect, links between species distribution records and environmental predictor variables to make predictions. Correlative models are an alternative to more complex mechanistic models that attempt to simulate the mechanisms considered to underlie the observed correlations with environmental attributes. This study explores the influence of the type and quality of the data used to calibrate correlative models. In terms of data type, the most popular techniques in use are group discrimination techniques, those that use both presence and absence locality data to make predictions. However, for many organisms absence data are either not available or are considered to be unreliable. As the available range of profile techniques (those using presence only data) appeared to be limited, new profile techniques were investigated and evaluated. A new profile modelling technique based on fuzzy classification (the Fuzzy Envelope Model) was developed and implemented. A second profile technique based on Principal Components Analysis was implemented and evaluated. Based on quantitative model evaluation tests, both of these techniques performed well and show considerable promise. In terms of data quality, the effects on model performance of false absence records, the number of locality records (sample size) and the proportion of localities representing species presence (prevalence) in samples were investigated for logistic regression distribution models. Sample size and prevalence both had a significant effect on model performance. False absence records had a significant influence on model performance, which was affected by sample size. A quantitative comparison of the performance of selected profile models and group discrimination modelling techniques suggests that different techniques may be more successful for predicting distributions for particular species or types of organism than others. The results also suggest that several different model design! sample size combinations are capable of making predictions that will on average not differ significantly in performance for a particular species. A further quantitative comparison among modelling techniques suggests that correlative techniques can perform as well as simple mechanistic techniques for predicting potential distributions.

A Geographic Information Systems (GIS) atlas of southern African freshwater fish was developed for the SADC countries from natural history collection specimens, hydrological, topographical and climatological data. The primary purpose of the development of the atlas of freshwater fish was the construction of a practical framework to transform vast amounts of existing biological data for use in research and management of aquatic resources. The database of freshwater fish collection specimens that was incorporated into the atlas, was developed in association with ALCOM (Aquatic Resources Management for Local Community Development Programme). The development of advanced computing and GIS technology has increased the scope of biological atlas projects by facilitating the integration of large amounts of spatial data to produce derived databases for specific applications. The atlas of freshwater fish was constructed using TNTmips GIS software as the most practical system available for managing and analysing biological data with a spatial component. The atlas contains 35 180 comprehensive distribution records of 735 species of fish. It has many applications as an inventory of ichthyofaunal spatial biodiversity, including those of conservation planning, environmental assessment and biogeographic research. Biogeographic studies have traditionally been subjective due to the logistical problems of working with large amounts of distribution data, although some small-scale quantitative research has been carried out in the past. The content of the atlas of freshwater fish is tested with respect to these previous studies, on known patterns of freshwater fish distributions, and the analytical capability of the atlas is tested and demonstrated with some new preliminary approaches to the analysis of freshwater fish distributions in southern Africa.

This study aimed to expand the existing knowledge on the diversity and distribution patterns of intertidal fishes in the Sardinia Bay MPA and adjacent open access areas. It focussed particularly on in intertidal fish communities along the Agulhas Bioregion coast which has been understudied, especially in recent years. Typical resident species belonging to the family Clinidae were the most abundant, conforming to previous studies. Species from the family Gobiidae were the second most abundant in this study but this family was not previously recorded as being abundant. Transient species were unimportant in the current study which is in contrast to previous studies in the region and suggests a change in species composition. Certain transient species utilised intertidal rockpools as part of their nursery areas in the Eastern Cape, as has previously been found around Algoa Bay. A decrease in species richness from east to west was recorded in this study which has been noted by previous authors and the diversity and distribution patterns of the intertidal fish in the current study conformed to patterns found previously. The position of the biogeographic boundary between the Agulhas and Natal Bioregions could not be confirmed but Wavecrest (along the Transkei coastline) appeared to be part of a transition zone rather than a fixed break. More sampling around this area is recommended to determine the location and understand the dynamic nature of this boundary. The fish species were found to be vertically distributed across the shore with most of the resident species being more abundant across the low shore while the transient species were more abundant in the middle to low shore pools. This vertical distribution has been found at many sites around the world. The volume of the pools proved to be the primary controlling factor while the effect of temperature on vertical distribution could not be demonstrated. The benefits of the Sardinia Bay Marine Protected Area on this unexploited community of fishes could not be demonstrated but the long term benefit of protection has yet to be shown. Results from this study suggest that despite the correspondence with general biogeographic trends, the intertidal fish community has changed in composition (at least in terms of transient species) during the last 30 years and the cause for these changes may in part be reduced recruitment from exploited linefish.

Thesis (MPH.) -- University of Limpopo, 2016
Introduction: During mid-November 2008, eleven acute watery diarrhoea cases with the suspicion of cholera like symptoms were detected by a diarrhoea surveillance system at Musina Hospital in Vhembe district - Limpopo Province, South Africa. These cases included eight Zimbabwean and three South African citizens. Laboratory test performed on stool specimens confirmed Vibrio cholerae serogroup 01 Ogawa as the causative pathogen for these reported acute watery diarrhoea cases. Within eight weeks of its onset, the outbreak spread to all the five districts of Limpopo. So far between 15 November 2008 and 01 June 2009, the cumulative number of cases of acute watery diarrhoea reported from five districts of Limpopo Province stands at 4634 including 30 confirmed cholera deaths with an overall case fatality rate of 0.65%. Of these reported cases, Vibrio cholerae has been laboratory confirmed in 656 samples. Methodology: A database was received from the Limpopo Department of Health having all reported cholera cases during the 2008 and 2009 outbreak in Limpopo Province. The data was analysed using STATA statistical software version 12 for windows (STATA Corporation, College Station, Texas). Results: The cholera affected all ages, but the geographic distribution of the disease was very heterogeneous in Limpopo Province. The highest and lowest numbers of cases were reported in Capricorn and Mopani districts, respectively. The majority of the cases 55% (N=2 542) were females. Children less than five years of age 14.2% (N=652) were less affected by the disease. About 73.8% of the cases were aged between O and 44 years. The first four weeks of cholera outbreak strictly included a day-to-day admixture of Zimbabweans and South Africans presenting in the health facilities. The outbreak then affected most South Africans after week five of the epidemic. Conclusion: The cholera outbreak has affected all the five districts of Limpopo Province in South Africa, and new cases continued to be reported until first week of June 2009. There was a link between the Zimbabwean and South African cholera outbreak in Limpopo province.

Bibliography: pages 100-108.
The snoek Thyrsites atun is an important fish predator in the southern Benguela region. It is exploited by both a handline and a demersal fishery. A survey of the Cape line fishery revealed that snoek line fishing effort is changing from the traditional harbour-based line-boat to the nomadic ski-boat. It was widely claimed that snoek catches are declining and that migration patterns are changing. Snoek constitute a by-catch of the hake-directed demersal fishery but nevertheless are seasonally important. The principle prey of snoek caught by handline off the Cape Peninsula were anchovy and mantis shrimp. Snoek caught in midwater trawls offshore were feeding primarily on anchovy, with pilchard, euphausiids and amphipods also important. Snoek trawled demersally had a more diverse diet, dominated by redeye roundberring, lightfish, lanternfish, hake, buttersnoek and euphausiids. Snoek were caught in the demersal environment throughout daylight hours, but may come off the bottom at night. The small degree of overlap between the diet of snoek caught demersally offshore and that of snoek caught in the pelagic zone, both inshore and offshore, indicates that snoek do not seem to move extensively on a diurnal basis between the two zones. Over the period 1970 to 1985 availability of snoek to the handline fishery was strongly seasonal, with catches peaking from May to July, although the traditional winter snoek run is a declining phenomenon along the South African coast. At Dassen Island, for which catch data have only been available since 1981, peak months were from November to January. The snoek seems to move offshore from July and is trawled demersally until September. The presence of snoek larvae offshore between June and September indicates an offshore spawning migration. With the exception of the summer presence in the region of Dassen Island, snoek appear to be present in the southern Benguela region between April and September. Handline catches of snoek have declined markedly since 1978, but demersal catches have remained more stable.

Dissertation (PhD)--University of Stellenbosch, 2007.
ENGLISH ABSTRACT: The taxonomic status of southern Africa’s rupicolous crag lizards (genus Pseudocordylus) was investigated. As considerable confusion exists in the literature regarding the type specimens and type localities of the various taxa, resolution of these problems were considered the starting point of the study. Examination of museum specimens allowed for the designation of lectotypes, alloparalectotypes and/or paralectotypes. Of particular relevance to this study was the rediscovery of Andrew Smith’s type specimens of P. m. melanotus and P. m. subviridis. Restriction of the type locality of P. m. subviridis, based on entries in Smith’s diary and journal, allowed for the confirmation of previous interpretations and definitions of the two taxa. The geographical distribution of the various taxa and populations was determined using an extensive locality database. Two kinds of molecular markers, namely allozymes and mitochondrial DNA, were used in an attempt to resolve taxon boundaries within the P. melanotus species complex. The allozyme analysis indicated that P. m. melanotus might be polyphyletic and comprised of two unrelated lineages. Furthermore, fixed allelic differences between parapatric populations of P. m. melanotus and P. m. subviridis, and between sympatric populations of P. m. subviridis and P. langi, suggested that all three forms might be considered full species, with the possibility of more cryptic species present in the complex. Pseudocordylus transvaalensis differed from most other populations by 1-3 fixed allelic differences, but was indistinguishable from the Nkandhla district (central KwaZulu-Natal) population of P. m. melanotus. There were no heterozygous individuals in a sample from Monontsha Pass (Qwa-Qwa), a population reportedly comprising P. m. melanotus and P. m. subviridis, as well as intermediates, and all specimens were assignable to P. m. subviridis. The allozyme study was, however, based on phenetic principles and for further taxonomic resolution a cladistic approach was required. An mtDNA analysis (16S rRNA gene) using Maximum Parsimony, Maximum Likelihood and Bayesian analyses was therefore conducted to determine phylogenetic relationships among species and subspecies and to re-assess the taxonomic status of forms in the P. melanotus species complex. The mtDNA analysis corroborated most of the results obtained in the allozyme analysis. Firstly, P. langi was again found to be basal. With the addition of P. microlepidotus and P. spinosus to the ingroup, it is now apparent that P. langi is the basal species in the genus. (Recent studies have indicated that P. capensis and P. nebulosus are not congeneric with Pseudocordylus.) Secondly, the 16S rRNA results confirm that P. m. melanotus, as presently construed, is comprised of two clades that are not sister groups. The northern populations of P. m. melanotus (Sabie and Lochiel) form a fairly deeply divergent clade that may represent a separate species. The Nkandla population was, however, found to cluster with the other southern P. m. melanotus populations and not with P. transvaalensis as was the case in the allozyme electrophoretic analysis. However, the most surprising result of the 16S rRNA analysis was the finding that both P. microlepidotus and P. spinosus are embedded within P. m. subviridis. This suggests that these two species evolved from within P. m. subviridis and may have been separated only recently, with rapid morphological divergence occurring, but with limited genetic differentiation. It is suggested that all of the above three taxa be provisionally treated as full species. There was also morphological support for the uniqueness of all groupings indicated by the mtDNA analysis. Pseudocordylus transvaalensis is characterized by its large size, unique dorsal and gular (black) colour patterns, as many as three horizontal rows of lateral temporal scales, a series of small scales posterior to the interparietal scale, and usually two subocular scales behind the median subocular on either side of the head. The various populations currently classified under the name P. melanotus are more difficult to separate, but P. m. melanotus and P. m. subviridis usually differ as follows: frontonasal divided in P. m. melanotus, undivided in P. m. subviridis (and most Northern melanotus); lateral temporals in two rows, upper more elongate versus single row of much elongated scales; longitudinal rows of dorsolaterals closely-set versus widely separated; femoral pores of females pit-like versus deep with secretory plug. Northern melanotus differs from Southern melanotus in usually having an undivided frontonasal scale and seldom having a small scale present behind the frontonasal. Pseudocordylus langi has unique dorsal and gular colour patterns (including a series of blue spots on the flanks), granular dorsals with 6-9 paravertebral rows of enlarged flat scales, high total numbers of femoral pores (25-34) and usually only five (smooth not keeled or ridged) infralabial scales on either side of the head. Pseudocordylus spinosus also has unique dorsal and gular colour patterns, spinose lateral scales, frontonasal longer than wide and excluded from the loreal scales, low total femoral pore counts (6-9), and females (not only males) have differentiated femoral scales. Both Principal Components Analysis (PCA) and Canonical Discriminant Analysis (CDA) distinguished four groups, namely P. transvaalensis, P. langi, P. spinosus and a P. melanotus/subviridis/microlepidotus cluster. A separate CDA of all P. melanotus populations partly distinguished between Southern melanotus and P. m. subviridis, and largely separated Northern melanotus; whereas a CDA of P. transvaalensis showed that all three allopatric populations are 100% distinguishable in morphological space. A Nested Clade Analysis indicated that fragmentation as well as range expansion played a role in the distribution of the P. melanotus species complex. This may be explained by climatic oscillations (high-low temperatures and wet-dry cycles) during the Cenozoic that caused habitat expansion and contraction. Based on the topology of the mtDNA phylogram it is apparent that the genus Pseudocordylus originated along the eastern escarpment. A P. langi-like ancestor may have had an extensive range along the eastern escarpment, with the Maloti-Drakensberg forming the southern limit of its range. During a subsequent rise in global temperatures, range contraction and fragmentation took place, leaving an isolated population in the south and one in the north. The southern population survived unchanged in the Maloti-Drakensberg refugium, but the northern population was forced to adapt to the warmer conditions. Thereafter, the northern form expanded its range again, but during a subsequent cooler period, range contraction occurred, resulting in an isolated north-eastern population in the Sabie-Lochiel area in Mpumulanga (Northern melanotus) and a western population. Relationships in the latter clade are not sufficiently resolved to allow further reconstruction of biogeographic history, but it is clear that a P. m. subviridis-like form became isolated in the south where it eventually came into contact with P. langi at high elevations. Pseudocordylus m. subviridis eventually extended its range southwestwards into the inland mountains of the Eastern Cape and Cape Fold Mountains to give rise to the P. microlepidotus complex. This cycle of range expansion and contraction may also account for the isolated populations at Suikerbosrand, Nkandhla district, and in the Amatole-Great Winterberg mountain region. Furthermore, it is suggested that P. spinosus originated from a P. m. subviridis-like ancestral population that became isolated on the lower slopes of the Drakensberg where terrestrial predation pressure resulted in a quick shift in morphology from fairly smooth body scales to a more spiny morphology.
AFRIKAANSE OPSOMMING: Die taksonomiese status van suidelike Afrika se rotsbewonende krans-akkedisse (genus Pseudocordylus) is ondersoek. Omdat daar aansienlike verwarring in die literatuur bestaan met betrekking tot die tipe monsters en die tipe lokaliteite van die verskillende taksa, is die oplossing van hierdie probleme as die beginpunt van hierdie studie geneem. Die bestudering van akkedismonsters in museums het dit moontlik gemaak om lektotipes, alloparalektotipes en/of paralektotipes aan te wys. Van besondere belang vir hierdie studie is die herontdekking van Andrew Smith se tipe monsters van P. m. melanotus en P. m. subviridis. Die beperking van die tipe lokaliteit van P. m. subviridis, gebaseer op inskrywings in Smith se dagboek en joernaal, het dit moontlik gemaak om vorige interpretasies en definisies van die twee taksa te bevestig. Die geografiese verspreiding van die verskillende taksa en bevolkings is bepaal deur middel van ’n omvattende lokaliteit databasis. Twee soorte molekulêre merkers, naamlik allosieme en mitokondriale DNS, is gebruik in ʼn poging om uitsluitsel te verkry oor die takson-grense binne die P. melanotus-spesiekompleks. Die allosiem-analise het daarop gedui dat P. m. melanotus moontlik polifileties mag wees en uit twee onverwante stamboom-vertakkings kan bestaan. Verder het vaste alleliese verskille tussen parapatriese bevolkings van P. m. melanotus en P. m. subviridis, en tussen simpatriese bevolkings van P. m. subviridis en P. langi, daarop gedui dat al drie vorme as volledige spesies beskou kan word, met die moontlikheid dat meer kriptiese spesies in die kompleks teenwoordig kan wees. Pseudocordylus transvaalensis het van die meeste ander bevolkings verskil met 1-3 vaste alleliese verskille, maar was ononderskeibaar van die bevolking van P. m. melanotus van die Nkandhla distrik (sentraal KwaZulu-Natal). Daar was slegs homosigote individue in ʼn steekproef van Monontsha Pas (Qwa-Qwa), ʼn bevolking wat volgens die literatuur P. m. melanotus en P. m. subviridis, sowel as intermediêre omvat, en alle monsters was toekenbaar aan P. m. subviridis. Die allosiemstudie is egter gebaseer op fenetiese beginsels en vir verdere taksonomiese oplossing is ʼn kladistiese benadering vereis. ʼn Mitokondriale DNS-analise (16S rRNS geen) wat gebruik maak van Maksimum Parsimonie-, Maksimum Waarskynlikheids- en Bayes-analises is daarom uitgevoer om die filogenetiese verwantskappe tussen spesies en subspesies te bepaal en om die taksonomiese status van vorme in die P. melanotus-spesiekompleks te herondersoek. Die mtDNS-analise het die meeste van die resultate van die allosiem-analise bevestig. Eerstens, P. langi is weer bevind om basaal te wees. Met die byvoeging van P. microlepidotus en P. spinosus tot die binne-groep het dit nou duidelik geword dat P. langi die basale spesie in die genus is. (Onlangse studies het aangedui dat P. capensis en P. nebulosus nie kongeneries met Pseudocordylus is nie.) Tweedens, die 16S rRNS resultate bevestig dat P. m. melanotus, soos tans vasgestel, saamgestel is uit twee klade wat nie sustergroepe is nie. Die noordelike bevolkings van P. m. melanotus (Sabie en Lochiel) vorm ʼn redelik diep divergente klaad wat ʼn afsonderlike spesie mag verteenwoordig. Dit is egter bevind dat die Nkandla bevolking saamgegroepeer het met die ander suidelike P. m. melanotus-bevolkings en nie met P. transvaalensis soos wat die geval was in die allosiem-elektroforetiese analise nie. Die mees verbasende resultaat van die 16S rRNS-analise was egter die bevinding dat beide P. microlepidotus en P. spinosus genestel was binne P. m. subviridis. Dit dui daarop dat hierdie twee spesies kon ontwikkel het vanuit P. m. subviridis en slegs onlangs van mekaar geskei het, toe vinnige morfologiese splitsing voorgekom het, maar met beperkte genetiese differensiasie. Dit word voorgestel dat al drie die bogenoemde taksa voorlopig as volledige spesies beskou word. Daar was ook morfologiese steun vir die uniekheid van al die groeperings wat die mtDNS-analise uitgewys het. Pseudocordylus transvaalensis kan uitgeken word aan sy bogemiddelde grootte, unieke dorsale en (swart) kleurpatrone op die keel, so veel as drie horisontale rye lateraaltemporale skubbe, ʼn reeks klein skubbe agter die interpariëtale skub, en gewoonlik twee subokulêre skubbe agter die middelste subokulêre skub op beide kante van die kop. Die verskillende bevolkings wat tans geklassifiseer word as P. melanotus is moeiliker om van mekaar te skei, maar P. m. melanotus en P. m. subviridis verskil gewoonlik soos volg: frontonasale skub in twee gedeel in P. m. melanotus, heel in P. m. subviridis (en in die meeste Noordelike melanotus); lateraal-temporale skubbe in twee rye, die boonste ry met verlengde skubbe teenoor ʼn enkele ry verlengde skubbe; longitudinale rye van dorsolaterale skubbe naby aan mekaar teenoor ver uit mekaar; femorale porieë van wyfies klein en vlak teenoor diep met sekreterende proppe. Noordelike melanotus verskil van Suidelike melanotus deurdat hulle gewoonlik ʼn heel frontonasale skub het en daar selde ʼn klein skub teenwoordig is agter die frontonasale skub. Pseudocordylus langi het unieke dorsale en keel-kleurpatrone (wat ʼn reeks blou kolle op die sye insluit), granulêre dorsale skubbe met 6-9 rye vergrote plat skubbe langs die rugsteen, ʼn groot totale aantal femorale porieë (25-34), en gewoonlik net vyf (glad, ongerif) infralabiale skubbe op elke kant van die kop. Pseudocordylus spinosus het ook unieke dorsale en keel-kleurpatrone, skerp laterale skubbe, frontonasale skub langer as wyd en nie in kontak met die loreale skubbe nie, klein totale aantal femorale porieë (6-9), en wyfies (nie net mannetjies nie) het gedifferensieerde femorale skubbe. Die Hoof-komponent Analise (HKA) en die Kanonieke Diskriminant Analise (KDA) het albei vier groepe geïdentifiseer, naamlik P. transvaalensis, P. langi, P. spinosus en ʼn P. melanotus/subviridis/microlepidotus groepering. ʼn Aparte KDA van alle P. melanotus bevolkings het gedeeltelik onderskei tussen Suidelike melanotus en P. m. subviridis, en die Noordelike melanotus is grootliks van die ander onderskei; terwyl ʼn KDA van P. transvaalensis daarop gedui het dat al drie allopatriese bevolkings 100% onderskeibaar in morfologiese ruimte is. ʼn Genestelde Klaad-Analise het aangedui dat fragmentasie, sowel as gebiedsuitbreiding, ʼn rol gespeel het in die verspreiding van die P. melanotus-spesiekompleks. Dit kan moontlik verklaar word deur die klimaatswisselinge (hoë-lae temperature en nat-droë siklusse) gedurende die Senosoikum wat habitat-uitbreiding en –verkleining veroorsaak het. Gebaseer op die topologie van die mtDNS filogram is dit duidelik dat die genus Pseudocordylus al langs die oostelike platorand ontstaan het. ʼn Voorouer soortgelyk aan P. langi kon ʼn uitgebreide gebied al langs die oostelike platorand gehad het, met die Maloti-Drakensberg wat die suidelike limiet van hierdie gebied gevorm het. Gedurende ʼn daaropvolgende toename in globale temperature het gebiedsverkleining en fragmentasie plaasgevind, wat ʼn geïsoleerde bevolking in die suide en een in die noorde tot gevolg gehad het. Die suidelike bevolking het onveranderd oorleef in die Maloti-Drakensberg skuilplek (“refugium”), maar die noordelike bevolking is geforseer om aan te pas in die warmer toestande. Daarna het die noordelike vorm se gebied weer uitgebrei, maar gedurende ʼn daaropvolgende koeler periode het gebiedsverkleining weer plaasgevind, met die gevolg dat daar ʼn geïsoleerde noord-oostelike bevolking in die Sabie-Lochiel-area in Mpumalanga (Noordelike melanotus) en ʼn bevolking in die weste was. Verwantskappe in die laasgenoemde klaad is nie voldoende opgelos om verdere rekonstruksie van die biogeografiese geskiedenis moontlik te maak nie, maar dit is duidelik dat ʼn vorm soortgelyk aan P. m. subviridis geïsoleer geraak het in die suide waar dit eindelik op hoë liggings in kontak gekom het met P. langi. Die gebied van P. m. subviridis is ook later suidweswaarts uitgebrei tot in die binnelandse berge van die Oos-Kaap en Kaapse Plooiberge om tot die ontstaan van die P. microlepidotuskompleks aanleiding te gee. Hierdie siklus van gebiedsuitbreiding en verkleining kan ook ʼn verklaring bied vir die geïsoleerde bevolkings by Suikerbosrand, Nkandhla distrik, en in die Amatole-Groot Winterberg-streek. Verder word voorgestel dat P. spinosus ontstaan het uit ʼn voorouerlike bevolking soortgelyk aan P. m. subviridis wat geïsoleerd geraak het op die laer hange van die Drakensberg waar die druk van aardsbewonende roofdiere tot ʼn vinnige verandering in morfologie vanaf redelik gladde liggaamskubbe tot ʼn meer skerppuntige morfologie gelei het.

Thesis (MSc)--University of Stellenbosch, 2006.
ENGLISH ABSTRACT: An understanding of the phylogeography and evolutionary processes involved in speciation is essential for the conservation and management of any particular species. To investigate the phylogeographic patterns in Agama atra from the Cape Fold Mountains (CFM), 98 individuals from 38 geographically close localities were analysed. In addition, to understand the phylogeographic associations between the CFM populations and the rest of Southern Africa, 18 specimens from 12 localities outside the CFM were also included. A total of 988 characters derived from two mitochondrial DNA fragments (control region and ND2) revealed 59 distinct haplotypes in the CFM. Parsimony, Bayesian and maximum likelihood analyses revealed four distinct clades associated with geography within the CFM. These clades were supported by a haplotype network and were defined as the Cape Peninsula clade, the Limietberg clade, the northern CFM clade and the central CFM clade. Analysis of molecular variance confirmed the high degree of genetic structure within the CFM, with more than 75% of genetic variation found among the geographic areas. SAMOVA and nested clade analysis (NCA) suggest that the central CFM clade may be more diverse than detected by the networks and the phylogenetic analyses. The processes that caused the four distinct genetic groups in the CFM are not yet clear. Using a speculative molecular clock estimate, the main cladogenesis of A. atra within the CFM took place, approximately ~6.5 - 9 MYA. This dating coincides well with the documented Miocene-Pliocene climate fluctuations which might have contributed towards the isolation among lineages. The genetic structure found in A. atra is also markedly congruent with what has been found in other taxa such as Mesamphisopus spesies, Potamonautes brincki, and Pedioplanis burchelli and this would further support vicariance as a main isolating factor here.
AFRIKAANSE OPSOMMING: ‘n Goeie begrip van die filogeografie en die evolusionêre gebeurtenisse wat verband hou met spesiasie is belangrik vir die bewaring en bestuur van enige spesie. Om die filogeografiese patrone in Agama atra van die Kaapse Plooiberge (KPB) te ontleed, was 98 individue van 38 nabygeleë lokaliteite geanaliseer. Tesame met bogenoemde monsters was 18 individue van 12 lokaliteite van buite die KPB ook geanaliseer om die filogeografiese verwantskappe tussen die KPB bevolkings en die res van Suidelike Afrika te ondersoek. Uit ‘n totaal van 988 karakters verkry uit twee mitochondriale DNS fragmente (die kontrole gebied en ND2) is 59 haplotipes gevind. Parsimonie en modelgebaseerde filogenetiese analises dui daarop dat vier groepe geassosieer met geografie binne die KPB voorkom. Die groepe word geondersteun deur ‘n haplotipe netwerk en word soos volg gedefinieer: ‘n Kaapse Peninsula groep, ‘n Limietberg groep, ‘n noordelike KPB groep en ‘n sentrale KPB groep. Analises van molekulêre variansie (AMOVA) bevestig die hoë graad van genetiese struktuur binne die KPB, met meer as 75% genetiese variasie gevind tussen die geografiese areas. SAMOVA en gesetelde groep analises (“NCA”) stel voor dat die sentrale KPB groep dalk meer variasie vertoon as wat die netwerk en filogenetiese analises vertoon. Die prosesse wat die vier genetiese groepe tot stand gebring het is nog nie bekend nie. Volgens ‘n spekulatiewe molekulêre klok berekening het die hoof kladogenese van A. atra binne die KPB ongeveer ~6.5 - 9 miljoen jaar (MJ) gelede plaasgevind. Hierdie datering stem goed ooreen met die gedokumenteerde Mioseen-Plioseen klimaat veranderinge wat isolasie van die groepe kon bewerkstellig het. Die genetiese struktuur van A. atra in the KPB is ook gevind in ander taksa soos Mesamphisopus spesies, Potamonautes brincki, en Pedioplanis burchelli en bevestig dus dat vikariansie hier die hoof faktor vir isolasie is.

Rock pools can be found in most rocky intertidal marine environments across the globe. Despite the vast body of literature describing the organization of ecological communities and biota inhabiting the greater rocky intertidal, very little effort has been given to rock pools. As a result they are far less understood than the adjacent emergent intertidal, particularly with respect to their fish communities. This is mostly due to the relative small size of rock pool fishes, their cryptic behaviour and morphologies, the relative difficulty in sampling intertidal fish utilizing conventional methods, and the low economic value of rock pool fishes. Rock pool fishes may have significant ecological value, as they are involved in structuring intertidal communities. Due to reduced environmental fluctuations within rock pools, these habitats may serve as crucial refuges from adjacent stressors. Furthermore, rock pools may play an important role in the early life histories of sub-littoral fish species that utilize these habitats as juveniles, some of which are valuable to fisheries as adults. It has been suggested that due to the lack of exposure at low tide, rock pools do not represent a true intertidal habitat, as organisms are not subject to the full range of environmental fluctuations seen in adjacent habitats. There is unequivocal evidence indicating that, like the surrounding emergent substrata, conditions in rock pools are highly regulated by the tidal cycle and that the degree of environmental fluctuations will vary greatly with intertidal height and degree of exposure of individual pools, much like patterns seen in adjacent habitats. Fishes inhabiting rock pools can be broadly categorised into groups based on their major zoographic provinces, life history traits and their behavioural affinities, on top of basic taxonomic categorizations. Global patterns indicate two main rock pool fish communities, those of Gondwanan origin and those of Laurasian origin. South African rock pools are relatively well studied from a taxonomic perspective compared to elsewhere, however, like the rest of the globe, factors influencing their fish communities are far less understood. The aim of this study was to determine which, if any, physical and biological rock pool characteristics have any significant influence on the Abundance, Diversity and Community of fishes at Goukamma MPA, South Africa. This site was chosen due to a lack of previous surveys of rock pool fishes at this site and because of a need for an inventory of faunal communities in protected areas in South Africa. The shoreline within the reserve is dominated by sandy shores and interspersed with mixed rock-based habitats. Aelonite platforms form mixed shores and are found along areas west of the Goukamma estuary. Hard, predominantly older Table Mountain Sandstone layers are found along the eastern shore near Buffalo Bay. Rock pools are found at both shore types. Aelonite platforms were formed geologically recently from sand dunes formed during the interglacial periods of the Pleistocene and as a result are relatively flat and easily eroded into circular pools by loose rocks. The hard table mountain sandstone pools formed in cracks and faults caused by geological tilting action, and tend to long and thin rather than circular. Fifty-five rock pools were sampled, to investigate the influence of spatial (Location and Headland), temporal (Season), abiotic (Area, Height, Depth, Rugosity) and biological (Rock, Algae,) characteristics of rock pools on the distribution, abundance, diversity and community composition of rock pool fishes. A total of 747 fishes, representing seven families and 16 species were collected, using a non-lethal anesthetic, clove oil. Clinus cottoides, Parablennius cornutus and Caffrogobius caffer were the most dominant species, together making up almost 85% of the fish community. Total fish Abundance was not found to significantly change with any of the variables. The Shannon-Wiener Species Diversity Index for the whole of Goukamma was 1.64, however, it differed significantly among Locations, was greatest in pools of larger Area, lower Heights and higher cover of Rock. Community was found to significantly change with Location and was significantly influenced by Area, Rugosity, Height and Depth. Rock pool fish communities in South Africa show clear biogeographical patterns. These patterns show five distinct bioregions along the South African coastline in that familial distributions tend to be broken by the same oceanographic barriers seen in the distributions of many other marine taxa. The results suggest that rock pool fishes tend to exhibit distinct preferences to pools of certain typology and will seldom move over even small distances in search of new pools. Overall the study followed past findings from studies of similar type, both within South African and elsewhere.

Despite the deteriorated state of health care in South Africa, the government remains committed to realising the right of every citizen to access health care, including good, quality and essential drugs. In recognising the availability of pharmaceutical facilities as a major component of access to health care, and the previous imbalances in the distribution of pharmaceutical structures and services, laws pertaining to the licensing and ownership of pharmacies were amended and promulgated in 2003 to address the distribution problem. In addition, regulations relating to a transparent priCing system on medicines and related sUbstances were introduced in 2004. These, coupled with factors influencing the choice of a pharmacy location, and the deficiencies in human resourges exercising an impact on both pharmacy and other health care personnel, have influenced the distribution and availability of pharmaceutical structures in South Africa from the year 2003 to 2008. OBJECTIVE: The main objective of this study was to investigate the availability and distribution of pharmaceutical structures registered with the South African Pharmacy Council, in South Africa, as of 2003 until 2008. METHOD: Data on the total number and geographical distribution of registered pharmaceutical structures in South Africa were obtained from the South African Pharmacy Council's register of pharmacies of August 2003, 2004, 2005, 2006, 2007 and 2008. The registered pharmaceutical structures were categorised according to their nature of services to the patient into "direct service" and "indirect service" (support) pharmacies. Availability was taken to refer to the actual presence of the pharmaceutical structures in relation to the demand for the services and measured quantitatively using population: provider ratios. The 'population' for indirect service pharmacies was taken as the direct service pharmacies and, the 'population' for direct seNice pharmacies was taken as the estimated population of the different geographical regions. RESULTS: The results revealed a 12% increase in the total number of registered pharmaceutical structures between the study years, to a total of 4227 pharmaceu'tical structures in 2008. Gauteng was identified as the province with the highest number of registered pharmaceutical structures, while the Northern Cape province contained the lowest number of registered pharmaceutical structures throughout the entire study period. The percentage of municipalities without any registered pharmaceutical structures decreased from 23% in 2003 to 19% in 2008. The indirect seNice pharmacies constituted 14% of the total number of registered pharmaceutical structures in South Africa. Most of these structures were situated in the province of Gauteng throughout the study period. National availability of these structures only improved for the manufacturing pharmacies. The registered direct seNice pharmacies increased by 13.2% to total 3642 pharmacies in 2008. Approximately 20% of the municipalities in the country (respectively 5.5% of the population) did not contain any registered direct seNice pharmacy in 2008. Most of these municipalities were situated in the KwaZulu-Natal province. The province of Gauteng contained the highest proportion (32%) of the direct seNice pharmaceutical structures. The decrease in the pharmacy per population ratio of the structures from 1: 14 547 people in 2003 to 1: 13 615 people in 2008 indicated an improvement in the availability of the structures. However, the improved availability did not take effect within each province as the Northern Cape, Mpumalanga and Gauteng provinces experienced an increase in the pharmacy per population ratio. CONCLUSION: The availability of registered pharmaceutical structures in South Africa improved between 2003 and 2008. However, the distribution of these structures remains geographically uneven and inequitable to the population of the country.
Thesis (M.Pharm. (Pharmacy Practice))--North-West University, Potchefstroom Campus, 2010.

Includes bibliographical references
Wild plants assist in supporting human livelihoods worldwide, both within traditional systems of medicine, and as economically useful plants. Indigenous to the Fynbos biome in the north-western part of the Western Cape, South Africa is the leguminous shrub, A. linearis (rooibos), which is extensively used as ethnomedicine by local communities, while also commercially grown and exported for the herbal tea market. Being a range-restricted species, climate change poses a threat to wild plants and their dependent communities, as well as the sustainability of the rooibos industry. Climate mediated impacts on rooibos are mostly substantiated by anecdotal evidence from commercial growers and local communities and have traditionally been insufficiently addressed. This study integrates predictive modelling and empirical data to provide important insights into rooibos' plant physiological functioning in the presence of climatic and environmental constraints. The aim is to determine whether there is evidence of climate change over the rooibos distribution area, how these climate anomalies are expected to affect the species distribution and to perform experimental studies by testing plant physiological functioning of A. linearis under changing climate conditions. Analysis of climate parameters important for rooibos production (rainfall frequency and intensity, temperature extremes and wind speed) have shown that plants will experience a shorter period of water availability during winter, and prolonged exposure to summer conditions (high temperatures and water stress) in the coming decades. Under these conditions, climate envelope modelling suggests that wild and cultivated rooibos types are at risk to lose between 49.8% and 88.7% in the extent of the bio-climatically suitable localities, most notably along the western and northern periphery of the rooibos production area by 2070. Plant physiological responses (growth analysis, gas exchange parameters and leaf carbon and nitrogen isotope ratios) to the assessed climate anomalies were measured in experimental studies at glasshouse and field scale. Specific adaptation mechanisms (increasing water use efficiency, developing a higher level of sclerophylly and altering the allocation of plant reserves) which helped seedlings to survive short term drought in the glasshouse were not able to offset more severe conditions in field settings. Finally, a comparison of wild and cultivated tea has shown an apparent adaptive advantage of wild tea to tolerate increased aridity with greater water economy, and more reliance on biological nitrogen fixation for N nutrition, indicating a potentially less severe scenario of range contraction for wild types than initially indicated. This study provides a more robust prediction of rooibos plant responses to climate change factors to enable more effective adaptive planning and conservation management in a changing climate.

Dissertation (PhD)--University of Stellenbosch, 2004.
ENGLISH ABSTRACT: Historically, isopods of the suborder Phreatoicidea were thought to be represented in southern Africa by four species belonging to the endemic genus Mesamphisopus. This taxonomy was based on poor collections and the extent of variation among and within populations were poorly understood. In the present study, intensive sampling was undertaken to determine the diversity, distribution and biogeography of phreatoicidean isopods within South Africa. Analyses of allozyme data and mitochondrial DNA sequences (from the 12S rRNA and protein-coding COI genes) were used to examine differentiation among populations, extricate species boundaries (in combination with morphometric and morphological data) and to elucidate the evolutionary relationships among taxa. Additionally, conservation units were identified among the sampled populations and conservation threats highlighted. First, genetic and morphometric differentiation was examined among populations identified morphologically as M. capensis. Collection localities spanned two mountainous regions in the Western Cape and these were separated by a coastal plain remnant. Five morphometrically and genetically distinct species were identified. These taxa are also geographically partitioned in two regions, which were regarded as Evolutionarily Significant Units. Differentiation among populations of the two regions, and similar patterns in other taxa, was attributed to Cenozoic sea-level fluctuations. Second, populations, variably assigned to M. abbreviatus or M. depressus, were examined to determine whether they were conspecific. A large geographic area was sampled to account for intraspecific differentiation. Limited morphometric discrepancies were observed, with individual populations being either similar to the M. abbreviatus or the M. depressus syntypes. Genetic support for the recognition of a cryptic species complex among the sampled populations was equivocal. Substantial genetic differentiation and a lack of gene flow were observed among all populations. Clear patterns of isolation by distance were not detected, and genetic structure appeared to be unrelated to geography or drainage systems. The mosaic pattern of relatedness among populations was best explained by stochastic demographic processes, such as extinction-recolonization events or population bottlenecks.Thirdly, detailed taxonomic descriptions and illustrations of six new species, identified genetically and morphometrically among the populations included in the above analyses, were provided. These species were largely distinguished from each other, and the four original species, using a combination of setation, mouthpart, pleopod and uropod features. Lastly, phylogenetic relationships among all ten recognized Mesamphisopus species, and an additional unresolved group of populations, were examined. MtDNA data partitions and a recoded allele frequency matrix were analysed independently and in combination. Topologies indicated unrecognized species-diversity within an unresolved group of populations. Evolutionary relationships, the identification of six biogeographic centres, and the dating of divergences using a relaxed Bayesian clock suggested that differentiation and speciation within Mesamphisopus was largely allopatric or vicariant and driven by Mesozoic sea-level and climate change. Chance long distance dispersal events would, in turn, explain spurious phylogenetic relationships and distributions. This study contributes significantly to the understanding of the diversity and the conservation of the little-studied southern African freshwater invertebrates. Moreover, this study is the first to investigate genetic and morphometric differentiation, and phylogenetic relationships, below the generic level within the Phreatoicidea; thus establishing a methodological and theoretical framework for species delineation and the accurate determination of biodiversity within individual phreatoicidean genera.
AFRIKAANSE OPSOMMING: Isopoda van die suborder Phreatoicidea was histories in suidelike Afrika verteenwoordig deur vier spesies wat almal aan die endemiese genus Mesamphisopus behoort. Hierdie taksonomie is op ’n beperkte hoeveelheid versamelings gebaseer en die omvang van variasie tussen (en binne) bevolkings was swak verstaan. In die huidige studie is ekstensiewe versameling onderneem om die verspreiding, diversiteit asook biogeografie van dié Isopoda in Suid Afrika te bepaal. Analises van allosiem data en mitokondriale DNS volgorderbepalings (van die 12S rRNS en die proteïenkoderende COI geen) was gebruik om differensiasie tussen bevolkings te ondersoek, om (in kombinasie met morfometriese en morfologiese data) spesiesgrense te bepaal asook om die evolusionêre-verwantskappe tussen taksa te definieer. Benewens word bewaringseenhede binne die studie-bevolkings geïndentifiseer en moontlike bedreigings uitgelig. Eerstens is genetiese en morfometriese differensiasie tussen bevolkings, wat as M. capensis geïdentifiseer is, ondersoek. Versamelingslokaliteite was versprei oor twee bergagtige streke in die Weskaap wat geskei word deur ’n voormalige kusvlakte. Vyf morfometries- en geneties-afsonderlike spesies is geïdentifiseer. Dié taksa was geografies geskei tot die twee streke, wat elk as ’n Evolusionêre Beduidende Eenheid (ESU) gesien kan word. Differensiasie tussen populasies van die twee streke en vergelykbare patrone binne ander taksa word aan Cenosoïese seevlak veranderings toegeskryf. Tweedens is bevolkings wat as M. abbreviatus óf as M. depressus geïdentifiseer kan word ondersoek om te bepaal of hulle konspesifiek is. Bevolkings is oor ’n groot geografiese gebied versamel om intraspesifieke variasie in aanmerking te neem. Beperkte morfometriese verskille is waargeneem – enkel bevolkings was morfometries identies aan of die M. abbreviatus of die M. depressus sintipes. Genetiese getuienis vir die herkenning van ’n kriptiese spesieskompleks was dubbelsinnig. Bevolkings is gekenmerk deur merkbare genetiese differensiasie en die afwesigheid van geenvloei. Duidelike bewys van isolasie-metafstand was nie waargeneem nie en genetiese struktuur was nie verwant aan geografiese ligging of riviersisteme nie. Die mosaïese patroon van verwantskappe is moontlik teweeg gebring deur stogastiese demografiese prosesse soos uitsterwing en hervestiging of deur afnames in bevolkingsgrootte.Derdens is omvattende taksnomiese beskrywings en illustrasies van ses nuwe spesies wat deur bogenoemde analises geneties en morfometries uitgelig was, verskaf. Dié spesies is van mekaar, asook die ander vier spesies onderskeibaar deur ’n kombinasie van setasie-, monddeel-, pleiopoot- en uropooteienskappe. Laastens is die filogenetiese verwantskappe tussen al tien herkende Mesamphisopus-spesies en ’n groep bevolkings waarvan verhoudings onseker was, ondersoek. MtDNS datastelle en ’n hergekodeerde alleelfrekwensie matriks is afsonderlike en in kombinasie geanaliseer. Topologië het onherkende spesies-vlak diversiteit binne die bogenoemde groep bevolkings aangedui. Evolusionêre verwantskappe, die herkenning van ses biogeografiese gebiede, en die bepaling van tye van divergensie (d.m.v. ’n ontspanne Bayesiaanse molekulêre klok) het aangetoon dat spesiasie binne Mesamphisopus grootliks allopatries was en deur Mesosoïese seevlak- en klimaatsveranderings teweeg gebring is. Toevallige lang-aftstand verspreiding kon dan eienaardige filogenetiese verhoudings en verspreidings verklaar. Dié studie lewer ’n wesenlike bydrae tot die kennis van die diversiteit en tot die bewaring van die onbestudeerde Suid Afrikaanse varswater ongewerweldes. Daarenbowe, is hierdie studie die eerste om genetiese en morfometriese differensiasie benede die genusvlak binne die Phreatoicidea te ondersoek; sodoende word die metodologiese en teoretiese raamwerk vir die herkenning van spesies en die akkurate beskrywing van diversiteit binne afsonderlike genera van die Phreatoicidea geskep.

This study identified the need to provide a proof of concept of the use and disaggregation of existing health data in order to study the cross-sectional and spatial distribution of HIV, tuberculosis and noncommunicable disease multimorbidity and the association with socioeconomic disadvantage at a South African, Western Cape Province and urban/intra-urban scale for 2008 and 2012. This study was framed within a health geography context and draws attention to the reality of health variations which are influenced by place-based effects, including the surrounding social, cultural and economic structural factors and mechanisms that, together, constitute the social determinants of health. However, in order to identify and understand these variations in health, access to health data that is able to be disaggregated by key characteristic and spatial scales, is essential. Therefore, this study utilised existing health data from the National Income Dynamics Study, a longitudinal study with a sample of approximately 28 000 people, to perform secondary data analysis using a positivist approach to research. This study found that the coupling of geospatial and health data is able to produce new health information and the graphical representation of data provides unique insights in health variations. Secondly, the burden of disease is not consistent between spatial scales which suggests variations in epidemiological profiles between sub-national geographies, thereby supporting the argument for the need of data disaggregation. Finally, the cross-sectional analysis of this study found multimorbidity to be associated with age, socioeconomic deprivation, obesity and urban areas, while the spatial analysis showed clusters (hot spots) of higher multimorbidity prevalence in parts of KwaZulu-Natal and the Eastern Cape, which compared with the socioeconomic disadvantage spatial pattern. Therefore, this study provides an example of the research needed to provide information to support policy improvement and enable the urban planning and public health professions to work together.

Chrysoblephus puniceus is an over-exploited linefish species, endemic to the coastlines off southern Mozambique and eastern South Africa. Over-exploitation and habitat loss are two of the biggest threats to the sustainability of fisheries globally. Assessing the genetic stock structure (a prerequisite for effective management) and predicting climate related range changes will provide a better understanding of these threats to C. puniceus which can be used to improve the sustainability of the fishery. Two hundred and eighty four genetic samples were collected from eight sampling sites between Ponta da Barra in Mozambique and Coffee Bay in South Africa. The mitochondrial control region and ten microsatellite loci were amplified to analyse the stock structure of C. puniceus. The majority of microsatellite and mtDNA pairwise population comparisons were not significant (P > 0.05) although Xai Xai and Inhaca populations had some significant population comparisons for mtDNA (P < 0.05). AMOVA did not explain any significant variation at the between groups hierarchical level for any pre-defined groupings except for a mtDNA grouping which separated out Xai Xai and Inhaca from other sampling sites. SAMOVA, isolation by distance tests, structure analysis, principle component analysis and spatial autocorrelation analysis all indicated a single population of C. puniceus as being most likely. The migrate-n analysis provided evidence of current driven larval transport, with net migration rates influenced by current dynamics.Two hundred and thirty six unique presence points of C. puniceus were correlated with seasonal maximum and minimum temperature data and bathymetry to model the current distribution and predict future distribution changes of the species up until 2030. Eight individual species distribution models were developed and combined into a mean ensemble model using the Biomod2 package. Winter minimum temperature was the most important variable in determining models outputs. Overall the ensemble model was accurate with a true skills statistic score of 0.962. Binary transformed mean ensemble models predicted a northern and southern range contraction of C. puniceus' distribution of 15 percent; by 2030. The mean ensemble probability of occurrence models indicated that C. puniceus' abundance is likely to decrease off the southern Mozambique coastline but remain high off KwaZulu-Natal. The results of the genetic analysis support the theory of external recruitment sustaining the KwaZulu Natal fishery for C. puniceus. While the high genetic diversity and connectivity may make C. puniceus more resilient to disturbances, the loss of 15 percent; distribution and 11 percent; genetic diversity by 2030 will increase the species vulnerability. The decrease in abundance of C. puniceus off southern Mozambique together with current widespread exploitation levels could result in the collapse of the fishery. A single transboundary stock of C. puniceus highlights the need for co-management of the species. A combined stock assessment between South Africa and Mozambique and the development of further Marine Protected Areas off southern Mozambique are suggested as management options to minimise the vulnerability of this species.

Thesis (MSc)--Stellenbosch University, 2008.
ENGLISH ABSTRACT: The Greater Cederberg Biodiversity Corridor (GCBC) is a large-scale conservation corridor situated in the south-western region of South Africa. Delineation of the GCBC was largely based on by vegetation data. The relevance of the GCBC for the conservation of the reptilian fauna in the area south of 31°S and west of 21°E is assessed in the present study. This entailed determining the GCBC’s coverage of regional reptile diversity patterns and assessing its potential conservation significance during possible climate induced changes in reptile distributions. Reptile species point distribution data from the preliminary (2007) SARCA (South African Reptile Conservation Assessment) database was used. Under-representation of the Tankwa Karoo in the dataset required a field survey of this region. Additionally, the biogeographical influence of the arid Tankwa Karoo Basin on the distribution of reptiles in the south-western districts of South Africa was investigated. Turnover across the Basin is high, species richness is lower than in surrounding mountainous areas and there are no species endemic to the area. The Tankwa Karoo Basin acts as a dispersal barrier for many reptile species occurring in the surrounding more mesic areas. At the same time, the ranges of a number of typical northern, arid adapted species extend southward along the Tankwa Plains. A number of species range extensions in the region are reported. Patterns of endemism, species richness and turnover were plotted from the point distribution data at quarter and eighth degree square resolution. Extensive sampling bias towards reserves and populated areas is apparent from the reptile species richness plots. This pattern is more pronounced for snakes than lizards. Reptile richness is particularly high along the north-south section of the Cape Fold Mountains and also relatively high along the south-western coast, peaking in the Lambert’s Bay area. The majority of the 20 reptile species endemic to the study area are associated with one of two identified centres of endemism: the Greater Cederberg area, or the narrow coastal zone stretching from the Lambert’s Bay area to the Cape Peninsula. An additional third set of endemics comprised of melanistic forms restricted to a number of different refugia, notably, Landroskop, the Cape Peninsula, Sladanha-Langebaan region, Piketberg Mountains and a confined area along the western section of the Cape Fold Mountains. Species richness and endemism patterns co-vary within the study area. Biotic regions were identified through hierarchical clustering of grid cells according to shared species occurrences. A Northern, Southern, Central and Western biotic region was identified. Classification tree methodology (CART) and Canonical Correspondence Analysis (CCA) were used to characterise defined biotic regions in terms of selected environmental variables. Four sets of species assemblages are described on the basis of these biotic regions – two major and two minor ones. Of the major assemblages the Northern assemblage can be described as an arid zone one and the Southern assemblage as a mesic zone one. The minor Central assemblage, comprising mainly rock-dwelling forms, represent evolutionary leftovers as a result of climate change induces cycles of contraction and expansion of arid and mesic faunas. The other minor one, the West Coast assemblage could be considered a sub-assemblage of the Northern one, with particular adaptation to the coastal climate. Environmental characterisation of the biotic regions reveals that these groupings are supported by an environmental signal. The contiguity of four distinct sets of reptiles, each with its own set of environmental requirements, in this relatively small geographic area clearly indicates that the southwestern region of South Africa is biogeographically complex. The GCBC incorporates the largely coinciding centres of endemism and richness along the West Coast and the greater Cederberg area. Although the centre of endemism for melanistic reptile forms, in the Saldanha-Langebaan area, falls just south of the GCBC boundary, the Corridor fulfils the requirements for effective conservation of reptiles in the area to a large degree. The north-south dispersal pathways provided by the Corridor along the Cape Fold Mountains is believed to be adequate to buffer climate change effects, however there is concern about its ability to contribute to the persistence of the assemblage associated with the narrow coastal zone in the west.
AFRIKAANSE OPSOMMING: Die Groter Cederberg Biodiversiteit Korridor (GCBK) is ‘n grootskaalse bewaringskorridor wat in die suid-westelike deel van Suid-Afrika geleë is. Die grense van GCBK is gebasseer op plantegroei data. In die huidige studie word die betekenis van die GCBK vir die bewaring van die reptiel fauna in die gebied suid van 31°S en wes van 21°O assesseer. Die mate waartoe die GCBK die patrone van reptieldiversiteit in die streek inkorporeer, asook die korridor se potensiaal om voorsiening te maak vir reptiel verspreidingsgebiede wat moontlik as gevolg van potensiële omgewingsverandering kan verskuif. Die beskikbare puntverspreidingsdata van die voorlopige (2007) SARCA (South African Reptile Conservation Assessment) databasis is gebruik. Swak verteenwoordiging van die Tankwa Karoo in die datastel het ‘n veldopname van die gebied genoodsaak. Verder is die biogeografiese invloed van die ariede Tankwa Karoo Kom op die verspreidingspatrone van reptiele in die suid-westelike deel van Suid-Afrika ook ondersoek. Die spesie omset van beide Noord na Suid en Wes na Oos oor die Tankwa is hoog, die spesierykheid is aansienlik laer as in die omringende bergagtige gebiede en daar is geen spesies wat endemies is tot die Tankwa Karoo nie. Die Tankwa Karoo Kom dien as ‘n barieêre teen spreiding vir sommige reptielspesies wat in die omringende gematigde gebiede voorkom. Terselfdertyd reik die verspreidings van ‘n aantal tipiese droogte aangepasde spesies vanuit die noorde suidwaarts langs die Tankwa Vlaktes. Nuwe verspredingsrekords wat ‘n paar spesies se gebiede uitbrei word ook raporteer. Die puntverspreidingsdata is geruik om die patrone van endemisme, spesierykheid en omset op kwart- en agtstegraad resolusie te plot. Spesierykheid kaarte toon ‘n duidelike neiging tot deegliker opnames in reservate en bewoonde gebiede. Hierdie patroon is meer opmerklik vir slange as akkedisse. Reptielrykheid is besonders hoog langs die noord-suid as van die Kaapse Plooiberge en ook relatief hoog langs die suid-wes kus met ‘n maksimum in die Lambertsbaai omgewing. Die meerderheid van die 20 reptielspesies wat endemies is aan die studie area is met een van twee geïdentifiseerde sentrums van endemisme geassosieer: die Groter Cederberg area óf die nou kussone wat vanaf Lambertsbaai tot Kaappunt strek. ‘n Derde stel endemiese spesies wat uit melanistiese vorme bestaan, is beperk tot ‘n aantal refugia, naamlik, Landroskop, Kaappunt, Saldanha- Langebaan omgewing, Piketberg berge en ‘n beperkte area langs die westelike dele van die Kaapse Plooiberge. Spesierykheid en endemisme patrone stem grootliks ooreen binne die studie area. Roosterselle is op grond van gedeelde spesiesamestellings met behulp van ‘n hieragiese groeperingsmetode (Incremental Sum of Squares) gegroepeer. Vier bio-areas, nl. ‘n Noordelike-, Suidelike-, Sentrale en Westelike bio-area is identifiseer. Klassifikasieboom metodologie (Classification and Regression Trees, CART) asook Kanoniese Annalises (Cannonical Correspondence Annalysis, CCA) is gebruik om hierdie geografiese areas in terme van ‘n aantal omgewingsveranderlikes te karakteriseer. Vier spesieversamelings, twee groter en twee kleiner versamelings, is in ooreenstemming met hierdie vier areas geïdentifiseer. Die Noordelike en Suidelike spesieversamelings is die groteres en kan beskryf word as die faunas van onderskeidelik ‘n ariede en gematigde sone. Die kleiner Sentrale versameling bestaan hoofsaaklik uit rots-lewende spesies en mag die evolusionêre oorblyfsels verteenwoordig van ariede en gematigde faunas waarvan die verspreidings herhaaldelik as gevolg van klimaatsveranderingsiklusse uitgebrei en gekrimp het. Die Weskus versameling is ook ‘n kleiner een en kan as ‘n sub-versameling van die Noordelike een beskou word, maar spesifiek tot die kus klimaat aangepas. Die klassifikasie van hierdie bio-areas word ondersteun deur die analiese van die omgewingsveranderlikes. Die feit dat vier kenmerkende versamelings reptiele, elk met sy besondere omgewingsvereistes, in hierdie relatief klein geografiese area ontmoet, dui daarop dat die suid-westelike deel van Suid-Afrika biogeografies kompleks is. Die GCBK inkorporeer die grootliks ooreenstemmende sentrums van endemisme en rykheid wat langs die Weskus en in die groter Cederberg area voorkom. Alhoewel die sentrum van melanistiese endemiese spesies, in die Saldanha-Langebaan omgewing, net buite die grense van die Korridor val, voldoen die GCBK grootliks aan die vereistes vir die effektiewe bewaring van reptiele in die gebied. Die voorsiening van noord-suid verspreidingsweë langs die Kaapse Plooiberge binne die Korridor word beskou as voldoende om die gevolge van klimaatsverandering te buffer. Daarinteen is daar kommer oor die vermoeë van die GCKB om ‘n doeltreffende bydrae te maak tot die voortbestaan van die spesieversameling wat met die nou kussone langs die Weskus geassosieer is.

Dissertation (PhD)--University of Stellenbosch, 2006.
ENGLISH ABSTRACT: This multi-disciplinary study compiled taxonomic and biogeographical data to elucidate the extant diversity of lechwe antelopes (Kobus leche complex), and reconstruct their evolutionary history. Their diversification has been confined to wetlands across the south-central Africa plateaux. Lechwes are specialist grazers in water meadow floodplains; these stenotopic habitat requirements are invoked to explain why their evolution is atypical of terrestrial large mammals. Combined analyses of morphological (171 adult males), genetic (208 genotyped individuals) and palaeo-environmental datasets, revealed a recent (Middle Pleistocene) pulse of speciation in the K. leche complex. Multivariate morphometric analyses revealed the presence of five distinct groups that could be tied to the geography of the region. Furthermore, the genetic analyses supported the existence of at least four of these lineages, which show significant population separation at the level of the mtDNA control region. Most of the differences among populations were confined to frequency differences among populations and Bayesian analyses strongly suggest that the pattern obtained is the result of the retention of ancestral haplotypes with limited female geneflow among the extant populations. Evolution of the five lineages identified by the morphological and population genetic analyses were further investigated by making use of additional genetic data (mtDNA cyt b, SPTNB, SRY, Protamine 1, and b-Fibrinogen) and a subset of the samples. Topologies were largely unresolved due to the recent common ancestry of the lineages. Following the Evolutionary Species Concept, which was motivated by a philosophical review, five allopatric species could be recognized (anselli, kafuensis, leche, robertsi and smithemani). A model of drainage evolution compiled disparate facets of biological and geological evidence to detail interlinked histories of wetlands and their biota across the south-central Africa plateaux. This wetland archipelago is recognized as a distinct biogeographical unit in its own right - the Katanga-Chambeshi region. Evolutionary diversification of lechwes represents a dominant biogeographical signal reflecting how the aquatic biota have evolved in tandem with palaeo-drainage dynamics across this evolutionary theatre. Delimitation of key events in lechwe and drainage evolution was refined by archaeological dating of the Victoria Falls Formation, to decipher when the Zambezi river eroded the Batoka gorge. Demographic expansion in K. leche s.s (early Middle Pleistocene) corresponds to dessication of Palaeo-Lake Makakgadikgadi while more recent phylogeographic signals correspond to the tenure of Palaeo-Lake Bulozi. These speciation events in the Middle Pleistocene preceded peripatric speciation of K. kafuensis that accompanied the morphosis of the Kafue Flats (from palaeo-lake to floodplain), when the Kafue River attained its modern topology. The present study highlights that Lechwes represent a biota of evolutionary vibrant clades, rich in endemic species. As ecologically-dominant species in wetlands, lechwes deserve priority conservation attention, which is challenged to perpetuate evolutionary and ecological processes across an archipelago straddling five countries.
AFRIKAANSE OPSOMMING: Die multidisiplinêre studie bring saam taksonomiese en biogeografiese data om die evolusionêre geskiedenis en huidige diversitiet van basterwaterbokke (Kobus leche kompleks) te verklaar. Hulle diversifikasie is beperk to vleilande regoor die suid-sentraal Afrika plato. Basterwaterbokke is gespesialiseerde grasvreters in grasvloedvlaktes; hierdie stenotipiese habitatsvereiste word voorgehou om te verduidelik hoekom die evolusie van hierdie diere atipies is vir terrestriële groot soogdiere. Gekombineerde analise van morfologie (171 volwasse manlike diere), geneties (208 genotipes) en plaeo-omgewings datstelle toon aan dat daar ‘n onlangse (middel Pleistoseen) pols van spesiasie plaasgevind het in die K. lechwe kompleks. Multivariate morfometriese analyses het aangetoon dat vyf verskillende groepe diere bestaan wat ook sin gemaak het op grond van geografiese ligging. Verdermeer, die genetiese analise het die bestaan van ten minste vier van hierdie lyne geondersteun wat betekenisvolle bevolkings isolasie vertoon het op die vlak van die mtDNA kontrole gebied. Meeste van die verskille tussen bevolkings was beperk to frekwensieverkille tussen die bevolkings en Bayesian analise het sterk aanduidings getoon dat die patroon wat gekry is die gevolg was van die behoud van voorvaderlike haplotiepes met beperkte vroulike geenvloei tussen die huidige bevolkings. Evolusie van die vyf lyne wat deur die morfologie en bevolkingsgenetika studies geidentifiseer is was verder ondersoek deur gebruik te maak van addisionele genetiese data (mtDNA cytb, SPTBN, SRY, Protamien 1, en b-Fibrinogeen) en ‘n subset van die monsters. Topologieë was hoofsaaklik onopgelos as gevolg van die kort tyd tot die onlangse gemeenskaplike voorouer van lyne. Deur die Evolusionêre Spesies Konsep aan te hang, wat gemotiveer is deur ‘n filosofiese oorsig, is vyf allopatriese spesies herken (anselli, kafuensis, leche, robertsi and smithemani). ‘n Model wat dreinerings evolusie voorstel het verskeie fasette van biologiese en geologiese bewyse saamgvat om die verbindingsgeskiedenis van vleilande en hulle biota oor die suidsentraal Afrika plato te beskryf. Die vleiland argipelago word herken as ‘n onafhanklike biogeografiese eenheid in sy eie reg – die Katanga-Chambeshi streek. Evolusionêre diversifikasie van basterwaterbokke verteenwoordig ‘n dominante biogeografiese sein wat voortsel hoe die akwatiese biota ontwikkel het in tandem met die palaeo-dreinerings dinamika in hierdie evolusionêre konsert. Die afbakening van sleutelgebeure in basterwaterbok en dreinerigsevolusie is beter toegelig deur argeologiese datering wat gebasseer was op die vorming van die Victoria Valle om te bepaal waneer die Zambezi rivier die Batoka skeurgroef gevorm het. Demografiese uitbreiding binne K. leche s.s (gedurende die vroë Middel Pleistoseen) stem ooreen met die uitdroging van Palaeo-Meer Makakgadikgadi terwyl meer onlangse filogeografiese syne ooreenstem met die ontstaan van Palaeo-Meer Bulozi. Hierdie spesiasie gebeure in die Middel Pleistoseen het die peripatriese spesiasie van K. kafuensis voorafgegaan wat die morfose van die Kafue Vlaktes vergesel het (van palaeo-meer na vloedvlakte), toe die Kafue Rivier sy huidige vorm aangeneem het. Die huidige studie het uitgelig dat basterwaterbokke verteenwoordig ‘n biota van evolusionêre energieke eenhede, ryk aan endemiese spesies. As ‘n ekologiese dominante spesie in vleilande, moet basterwaterbokke as ‘n prioriteit gesien word in bewaring, waar dit dan die geleentheid sal hê om voort te bou op die evolusionêre en ekologiese prossese van die archipelago wat oor vyf lande strek.

The most recent study on cetaceans in Algoa Bay, South Africa, was conducted over 14 years ago. Consequently, knowledge of the cetacean species visiting this bay is currently based on incidental observations and stranding data. A number of developments in recent years: a deepwater port, proposed oil refinery, increased boating and fishing (commercial and recreational), a proposed Marine Protected Area, and the release of a whale-watching permit, all of which may impact these animals in some way, highlight the need for a baseline study on cetaceans. Therefore, the aim of this study was to determine the spatial and temporal distribution, and habitat preference of cetaceans in Algoa Bay. Boat-based surveys were conducted monthly between March 2009 and July 2010. At each sighting the GPS location, species, group size and composition, and behaviour were recorded. Using GIS, the sighting data was related to data layers of geographical variables such as sea surface temperature, depth and sea-floor substrate. Approximately 365 hours of search effort were completed over 57 surveys, with a total of 346 sightings. Species observed were: southern right whales (Eubalaena australis), humpback whales (Megaptera novaeangliae), Bryde’s whales (Balaenoptera brydei), Indian Ocean bottlenose dolphins (Tursiops aduncus), Indo-Pacific humpback dolphins (Sousa chinensis), and longbeaked common dolphins (Delphinus capensis). Southern right whales were observed during austral winter, utilising the shallow, protected areas of the bay as a mating and nursery ground. Humpback whales were also recorded extensively during winter, in more offshore waters, with a significant number of mother-calf pairs sighted. Bryde’s whales were recorded in offshore waters during summer and autumn, where they were primarily observed travelling and foraging. Bottlenose dolphins were the most prolific species sighted. They were recorded year-round throughout the inshore waters of the bay, with large group sizes (up to 500 animals), and displayed a wide variety of behaviours. Humpback dolphins were observed in extremely shallow and inshore waters (mean bottom depth of 6.6 m) along the south-west corner of the bay, in small groups of approximately three individuals. Common dolphins were the least observed species, and were mainly observed foraging in large groups of up to 800 individuals. The results of this study indicate how cetaceans utilise the bay in significantly different ways. Geographical and anthropogenic factors have influenced the spatial and temporal distribution of these animals and have resulted in habitat preferences, as well as potential key habitats, in the bay. Thus, this study has provided baseline information for future research and for better informed conservation and management strategies in Algoa Bay.

Thesis (MSc)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: In the present study I examined the phylogeography of the rupicolous Cape girdled lizard, Cordylus cordylus. Samples were collected across the species distribution range from 63 localities in the Eastern and Western Cape and Free State provinces of South Africa, yielding a total sample size of 207 specimens. Four DNA loci, two nuclear (PRLR, PTPN12) and two mitochondrial (16S rRNA, ND2), were sequenced. Bayesian inference, maximum likelihood and maximum parsimony methods were employed to test evolutionary relationships among populations, followed by population structure analyses, divergence time estimations and niche modelling. My results confirm the species monophyly and revealed the presence of two distinct clades. Clade 1 comprised specimens from the western and southern portions of the Western Cape coast, while clade 2 comprised specimens from the southern and eastern Cape coast and adjacent interior of the Eastern and Western Cape and Free State provinces. An area of sympatry between the two clades was observed in the Breede river valley. The divergence time estimates revealed an Early Pliocene (4.31 Ma), Late Miocene (6.01 Ma) divergence for each of the two clades retrieved. Phylogeographic data suggest that clade 1 is younger (lower haplotypic and nucleotide diversity), in comparison to clade 2. Furthermore, the niche modelling shows that C. cordylus occupies a wide range of unfavourable habitats. The absence of marked phylogeographic patterning within clades is very uncharacteristic for a rupicolous vertebrate species. The ecological pliability and generalist nature of C. cordylus presumably contributed to the observed phylogeographic pattern and have facilitated the absence of within clade differentiation. Moreover, I suggest that microclimatic variables, rather than geographic barriers influence the genetic structuring of C. cordylus.

Thesis (PhD)--Stellenbosch University, 2008.
ENGLISH ABSTRACT: The order Macroscelidea has a strict African distribution and consists of two extant subfamilies, Rhynchocyoninae with a single genus that includes three species, and the Macroscelidinae represented by the remaining three genera, Elephantulus that includes 10 species, and the monotypic Macroscelides and Petrodromus. On the basis of molecular, cytogenetic and morphological evidence, Elephantulus edwardii (Cape rock elephant-shrew), the only strictly South African endemic species, was shown to comprise two closely related taxa. A new Elephantulus taxon, described here is reported for the first time. It has a restricted distribution in the central Nama Karoo of South Africa. Apart from important genetic distinctions, Elephantulus sp. nov. has several relatively subtle morphological characters that separate it from E. edwardii. Molecular sequences from the mitochondrial cytochrome b gene and the control region of E. edwardii sensu stricto suggests the presence of a northern Namaqua and central Fynbos clade with four evolutionary lineages identified within the latter. The geographic delimitation of the northern and central clades corresponds closely with patterns reported for other rock dwelling vertebrate species indicating a shared biogeographic history for saxicolous taxa in South Africa. Elephantulus rupestris (western rock elephant-shrew) and Macroscelides proboscideus (round-eared elephant-shrew) are two taxa with largely overlapping distributions that span the semi-arid regions of South Africa and Namibia. Based on mitochondrial DNA sequence data E. rupestris has a structured genetic profile associated with a habitat of rocky outcrops compared to M. proboscideus that inhabits gravel plains, where the pattern is one of isolationby– distance. Chromosomal changes, apart from heterochromatic differences, are limited to variation in diploid number among elephant-shrew species. These range from 2n=26 (E. edwardii; E. rupestris; Elephantulus sp. nov.; E. intufi; E. brachyrhynchus and M. proboscideus) to 2n=28 in both Petrodromus tetradactylus and E. rozeti to 2n=30 in E. myurus. Cross-species chromosome painting (Zoo-Fluorescence in situ hybridization or zoo-FISH) of E. edwardii flow-sorted probes that correspond to the five smaller sized autosomes (8-12) and the X chromosome showed no evidence of synteny disruption among Elephantulus sp. nov., E. intufi, E. myurus, P. tetradactylus and M. proboscideus, and reinforced the G-banding observations underscoring the conservative karyotypes in these species. A comprehensive phylogeny including all described elephant-shrew species is presented for the first time. A multigene supermatrix that included 3905 bp from three mitochondrial (12S rRNA, valine tRNA, 16S rRNA) and two nuclear segments (Von Willebrand factor [vWF] and exon 1 of the interphotoreceptor retinoid binding protein [IRBP]) was analysed. Cytogenetic characters, previously described morphological, anatomical and dental features as well as allozyme data and penis morphology were evaluated and mapped to the molecular topology. The molecular findings did not support a monophyletic origin for the genus Elephantulus and suggests that both the monotypic Petrodromus and Macroscelides should be included in Elephantulus. Molecular dating suggests that an arid-adapted Macroscelidinae lineage dispersed from east Africa at ~11.5 million years ago via the African arid corridor to southwestern Africa. Subsequent speciation events within the Macroscelidinae are coincidental with three major periods of aridification of the African continent.
AFRIKAANSE OPSOMMING: Die orde Macroscelidea het ’n verspreiding beperk tot Afrika en sluit twee bestaande subfamilies in, die Rhynchocyoninae wat drie spesies binne ’n enkele genus insluit en die Macroscelidinae verteenwoordig deur drie genera, Elephantulus (10 spesies) en die monotipiese Macroscelides en Petrodromus. Gebaseer op molekulêre, sitogenetiese en morfologiese bewyse, bestaan E. edwardii, tot op datum die enigste streng endemiese Suid- Afrikaanse klaasneusspesie, uit twee nabyverwante taksa. Die nuwe Elephantulus takson, hierin beskryf, het ’n beperkte verspreiding in die sentraal Nama Karoo van Suid-Afrika. Afgesien van belangrike genetiese bewyse wat die beskrywing van die nuwe spesie ondersteun, word Elephantulus sp. nov. gekenmerk deur ’n aantal subtiele morfologiese karakters wat dit onderskei van E. edwardii. Binne E. edwardii sensu stricto, het mitochondriale molekulêre volgordes beduidende substruktuur aangedui regoor die spesies se verspreiding. Die data het die teenwoordigheid van ’n noordelike Namakwa en sentrale Fynbos klade aangetoon met vier evolusionêre lyne binne die laasgenoemde. Die geografiese skeiding van die noordelike en sentrale klades stem grootliks ooreen met patrone in ander rotsbewonende vertebraat spesies, wat op ’n gedeelde biogeografiese verlede in Suid-Afrika dui. Elephantulus rupestris (westelike klipklaasneus) en Macroscelides proboscideus (ronde-oor klaasneus) is twee taksa met verspreidings wat grootliks oorvleuel in die semi-woestyn streke van Suid-Afrika en Namibië. Mitochondriale DNS volgorde-bepaling dui op ’n gestruktueerde genetiese profiel binne E. rupestris, geassosieer met ’n habitat van rotskoppies, in vergelyking met ’n isolasie-deur-afstand patroon wat M. proboscideus, wat op gruisvlaktes aangetref word, karakteriseer. Chromosoom verandering, afgesien van heterochromatiese verskille, is beperk tot ’n strukturele verandering van ‘n diploïede getal van 26 (E. edwardii; E. rupestris; Elephantulus sp. nov.; E. intufi; E. brachyrhynchus en M. proboscideus) tot 2n=28 in beide Petrodromus tetradactylus asook E. rozeti en 2n=30 in E. myurus. Kruis-spesies chromosoom fluoressent hibridisasie (“zoo-FISH”) van die vloei-sorteerde merkers toegewys tot die vyf kleiner grootte outosome (8-12) asook die X chromosoom van E. edwardii tot metafase chromosome van Elephantulus sp. nov., E. intufi, E. myurus, P. tetradactylus en M. proboscideus het geen bewyse getoon van sintenie-verbreking nie en versterk G-bandbepaling waarnemings wat die konserwatiewe kariotipes in hierdie spesies ondersteun. ‘n Volledige evolusionêre filogenie, verteenwoordigend van alle erkende klaasneusspesies, word vir die eerste keer voorgestel. As sulks is ’n multigeen supermatriks wat gebaseer is op 3905 bp van drie mitochondriale (12S rRNA, valien tRNA, 16S rRNA) en twee nukluêre segmente (Von Willebrand faktor [vWF] en ekson 1 van die interfotoreseptor-retinoïed-bindende proteïen [IRBP]) ingesluit. As toevoeging, is nuwe sitogenetiese data, voorheen beskryfde morfologiese, anatomiese en dentale karakters sowel as data van allosieme-analises en penis morfologie ge-evalueer en nie-molekulêre ondersteuning aangedui op die molekulêre topologie. Die molekulêre bevindinge ondersteun nie ’n monofiletiese oorsprong vir Elephantulus nie en stel voor dat beide die monotipiese Petrodromus en Macroscelides ingesluit moet word in die genus Elephantulus. Molekulêre datering stel voor dat ’n dor-aangepasde Macroscelidinae lyn versprei het vanaf oos Afrika ~11.5 miljoen jaar gelede deur die “droeë Afrika korridor” tot in suidwestelike Afrika. Verdere spesiasie gebeurtenisse binne die Macroscelidinae kan nouliks geassosieer word met drie groot periodes van verdorring in Afrika.

Complaints of crop damage by cranes on planted maize in the North Eastern Cape, South Africa, have been increasing since the mid-1990‘s, and in some instances severe losses have been reported. Crop damage by the Grey Crowned Crane Balearica regulorum regulorum near the town of Maclear (31º04´S 28º22´E), has been quantified over two growing seasons, and assessed relative to losses caused by foraging Cape Crows Corvus capensis and other feeding damage assumed to be caused by insects. Twelve fields were selected based on previous patterns of crop depredation. Maize seed in seven of the fields was treated with the chemical ‗Gaucho‘ and five fields were planted with untreated maize. In order to determine the source of losses, twenty quadrats (4 m x 4 m) randomly distributed within each field were visited on average every second day, for a period of up to twenty eight days. Results indicate that seed treatments do act as a deterrent to feeding by both cranes and crows, however crane damage is generally insignificant compared to other sources of damage. My study also reviewed past sightings data of the Grey Crowned Crane in an effort to determine if the conversion of former grassland to plantations in this region may have increased foraging activity in maize fields. The data did not allow for clear-cut conclusions regarding changes in distribution or population trends. Conclusions provide direct input into the management of agricultural areas by enabling landowners to take steps to mitigate crop damage. These mitigation measures may either involve the application of seed treatments, or the planting of low risk crops in high risk areas. Future studies should consider the ppossible detrimental effects of chemical seed treatments on crane biology.

It was previously thought that the South African chokka squid Loligo reynaudi is exclusively an inshore, shallow water spawner. Although spawning mostly within shallow bays (<60 m) the presence of squid eggs in trawls at depths up to 130 m indicates this species frequently makes use of deeper spawning areas on the mid-shelf. The extent of mid-shelf spawning (referred to as deep spawning) and the contribution to recruitment has yet to be assessed. Studies have shown mid-shelf bottom temperature to vary considerably from those inshore, suggesting chokka squid spawn in two very different oceanographic environments. Considering these apparent environmental differences, what leads to the mid-shelf environment becoming a suitable spawning habitat? Does a suitable benthic habitat, required for the attachment of egg pods, occur on the mid-shelf? These questions are not only important for determining the extent of deep spawning, but also to the understanding of factors “driving” deep spawning. The fate of deep spawned hatchlings is another unknown. It has been proposed that the main chokka squid inshore spawning grounds are positioned to exploit the net westward currents on the Eastern Agulhas Bank, i.e. paralarvae would be transported west from the hatching site to the cold ridge, an area of high primary and secondary productivity on the Central Agulhas Bank. This concept has come to be known as the Western Transport Hypothesis. Lagrangian ROMS-IBMs (regional ocean model system – individual-based model) predict the net westward transport of paralarvae from both the inshore and deep spawning grounds, to the cold ridge. These simulations were used to investigate the transport of hatchlings to the cold ridge feeding grounds before the exhaustion of yolk reserves. The fate of paralarvae on reaching the feeding grounds has not yet been investigated. This work has contributed new knowledge to our understanding of deep spawning and its role in recruitment. Specific aims of this study were to (1) determine the extent, range and importance of the deep spawning grounds relative to those inshore; (2) investigate the deep spawning ground habitat (Agulhas Bank mid-shelf) morphology and oceanographic environment; (3) determine the transport and survival of deep spawned hatchlings; and (4) investigate the origin and distribution of chokka squid paralarvae on the Agulhas Bank. The extent, depth range and importance of the deep spawning grounds, relative to those inshore was assessed using 23 years of demersal trawl survey data. Data for both the west and south coasts of South Africa were examined for egg capsules. No spawning was found on the west coast. Data showed that chokka squid preferred the Eastern Agulhas Bank for spawning. Spawning occurred not only inshore but also on the mid-shelf extending to depths of 270 m near the shelf edge. The majority of deep spawned eggs however, were found in the depth range 71-130 m. Squid egg density markedly decreased beyond 70 m, suggesting delineation between the inshore and deep spawning grounds. Total egg biomass calculations for depths shallower and deeper than 70 m indicated the coastal area to be strongly favoured, i.e. 82 vs. 18%. These results contest the commonly accepted notion that chokka squid is an inshore spawner and redefine the spawning grounds to extend across the shelf. Apart from an initial study investigating bottom temperature on the mid-shelf, very little is known about the deep spawning habitat. St Francis Bay, a commonly used spawning location, was chosen as a demonstration area for further study. The deep spawning grounds (71-130 m) were mapped and benthic habitat described from underwater video footage. A study investigating cross-shelf bottom conditions was undertaken off Thys Bay. CTD data were used to compare seasonal bottom temperature and oxygen on the St Francis Bay inshore and deep spawning grounds. Squid movement between the two spawning habitats was assessed using filament tagging. Predation and fishing pressure across the spawning grounds was reviewed. The mid-shelf benthic habitat was found to be similar to that inshore and available for spawning. Despite the generally colder bottom temperatures on the mid-shelf, this study showed that bottom temperature in deeper waters can at times be warmer than inshore. Although mid-shelf warming events lasted from a few hours to a number of days, they resulted in similar conditions to those on the inshore spawning grounds. It is likely these events act to expand or shift spawning habitat. The movement of squid between the two spawning habitats makes it possible for them to seek patches of warm bottom water with appropiate substrate. This suggests they are spawning habitat opportunists. Predation and fishing pressure appear to be higher on the inshore spawning grounds. It is feasible that this also forces spawners to seek out more favourable habitat offshore. An individual-based model was used to predict the fate of mid-shelf and inshore hatched paralarvae. Within the model, both the highly productive cold ridge and inshore spawning grounds were considered feeding or nursery areas. Paralarvae were released from six inshore and six deep spawning sites, spanning the coast between Port Alfred and Knysna. All paralarvae not reaching the feeding areas before the exhaustion of yolk-reserves (≤5 days), not retained within the feeding grounds (≥14 days), and not retained on the Agulhas Bank after exiting the feeding grounds were considered lost. This work illustrated the dependence of paralarval transport success on both spawning location and time of hatching, as established in earlier studies. The current IBM has expanded on initial work, emphasizing the importance of the cold ridge and inshore spawning grounds as nursery areas for deep and inshore spawned paralarvae, respectively. This work has highlighted the complex interactions between processes influencing recruitment variability for chokka squid. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off Tsitsikamma, and the beneficial currents during this period, it can be concluded deep spawning may at times contribute significantly to recruitment. This is particularly true for years where the cold ridge persists into winter. Data on chokka squid paralarval distribution are scarce. Paralarval distribution and abundance, in relation to Agulhas Bank oceanography, was investigated using bongo caught paralarvae and corresponding oceanographic data. Individual-based models (IBMs) were used to predict the origin or spawning site of the wild caught paralarvae, with reference to inshore versus deep spawning. Although failing to predict realistic points of origin, this study provided evidence to support a number of scenarios previously assumed to influence chokka squid recruitment. First is the possible influence of coastal upwelling on the retention, and hence spatial distribution, of paralarvae on the inshore spawning grounds. The second factor thought to impact recruitment is the loss of paralarvae from the Agulhas Bank ecosystem. This study confirmed the removal of paralarvae from the Eastern Agulhas Bank due to Agulhas Current boundary phenomena and resultant offshelf leakage. In addition, data suggested that the formation of the cold ridge could enhance retention on the Central Agulhas Bank, and so prevent offshelf leakage from the Central and Western Agulhas Bank. A synthesis of the main conclusions is presented. Implications of the findings and directions for future research are discussed.

Thesis (MSc)--University of Stellenbosch, 2005.
ENGLISH ABSTRACT: This project consists of two botanical investigations in an agricultural area of the Western Cape Province. A farm known as De Rust, in the Elgin Valley, was used to sample the geographic location, density, height and life stage of six prominent invasive plant species in various land-use categories. In the first investigation, the density, height and age structures of the six invasive species populations were analyzed. The density distribution of the six species was also displayed cartographically. Species were then ranked according to the potential threat that they pose to the conservation of the remaining natural areas on the farm. Results indicated that Acacia mearnsii and Acacia saligna are the major invaders at De Rust and that Hakea sericea can be considered as an emerging invader. The second investigation explores the statistical relationship between the various land-use categories and density, height and age of the six prominent invaders identified in the first investigation. The loglikelihood ratio analysis of observed frequencies resulted in statistically significant (P<0.01; P-values range between 1.35 x 10-3 and 2.7 x 10-224) relationships between certain land-use types and certain invasive species. A conclusion was reached that it could be useful to include land-use categories in simulation models of invasive plant species distribution and spread.
AFRIKAANSE OPSOMMING: Hierdie projek behels twee botaniese ondersoeke in ‘n landbou gebied van die Weskaap. Die plaas bekend as De Rust, in die Elgin Vallei, was gebruik vir die versameling van data te doen met die geografiese ligging, plant digtheid, lengte en lewens stadium van ses prominente indringer plant spesies in verskeie landgebruik kategorieë. Die digtheid, lengte en ouderdomstruktuur van ses indringerspesies was in die eerste ondersoek geanaliseer. Die verspreiding van digtheid was ook in kaarte uitgelê. Spesies was daarna volgens hulle potentiële dreiging teen die bewaring van oorblywende natuurlike dele van die plaas in ‘n rangorde geplaas. Resiltate dui aan dat Acacia mearnsii en Acacia saligna die belangrikste indringer plante op De Rust is en dat Hakea sericea as ‘n opkomende indringer beskou kan word. Die tweede ondersoek kyk na die verhouding tussen verskeie grondgebruik kategorië en die digtheid, lengte en ouderdom van die ses prominente indringer spesies wat in die eerste ondersoek identifiseër is. ‘n Log tipe ratios ontleding van bewaarde frekwensies het ‘n statisties belangrike uitkoms gehad (P<0.01; P-waardes tussen 1.35 x 10-3 en 2.7 x 10-224) vir die verhoudings tussen sekere grondgebruik tipes en sekere indringer spesies. Die gevolgtrekking was dat dit handig mag wees om grondgebruik kategorieë in simulasies van indringer plant verspreiding te gebruik.

The dispersal of freshwater fishes in the Cape Floristic Region of South Africa has been attributed to river capture events and confluence of rivers during sea level regression. The role of low drainage divides and inter-basin water transfers have received less attention. A unique lineage of Galaxias zebratus (hereafter the Joubertina galaxias) occurs in two currently isolated river systems, the Gamtoos and Krom. The present study mapped the distribution of the Joubertina galaxias and used mitochondrial and nuclear DNA sequences to assess the processes that could have influenced its current distribution pattern. Analyses of both mitochondrial cytochrome ♭ and nuclear (S7) sequences revealed that observed genetic differentiation cannot be explained by isolation between the Gamtoos and Krom River systems. No genetic differentiation was found between the Krom River System and the Twee River (a tributary of the Gamtoos River System). Shallow genetic differentiation (0.4% for cytochrome ♭ and 0.3% for S7) was found between the Krom and the remaining populations in the Gamtoos River System. High levels of genetic structuring were observed within the Gamtoos River System with most tributaries having one or more unique alleles. Inter-basin dispersal during pluvial periods or recent human mediated translocation seems to be the most plausible explanations for presence of the Joubertina galaxias in the Krom River System. The present study also assessed the threats and habitat preferences of the Joubertina galaxias, and an evaluation of the conservation status of this lineage was done. The Joubertina galaxias is threatened mainly by alien fish invasion, habitat loss and loss of genetic diversity due to fragmentation of its populations. Due to its very restricted geographic range, small known population sizes and the intensity of threats to this lineage’s survival, this lineage has been assessed as Endangered. The lineage has a restricted Area of Occupancy (AOO) and Extent of Occurrence (EOO). The extent of occurrence has declined in all tributaries and is continuing to decline in all except two tributaries that are secure. The lineage may have had natural fragmentation among its populations, but recent threats have completely isolated the populations. The threats affect the lineage’s survival potential in the four tributaries which have small populations that are not presently viable. The densities observed for the Joubertina galaxias ranged from 0.16 - 1.3 fish /m² and the number of mature individuals for the whole population seems to be less than 2500 mature individuals. There is therefore a need for specific conservation actions to ensure the long-term survival of this unique lineage.

When considering the large amount of work done on dune ecology, and that a number of the classical ecological theories originate from work on dunes, it is apparent that there remains a need for physiological and mechanistic explanations of dune plant phenomena. This thesis demonstrated that in the extreme coastal environment dune plants must survive both high rates of burial (disturbance), and low nutrient availability (stress). The ability of four species to respond to these two factors corresponded with their position in a vegetation gradient on the dunes. A low stem tissue density was shown to enhance the potential stem elongation rate of buried plants, but reduced the maximum height to which a plant could grow. Such a tradeoff implies that tall light-competitive plants are able to survive only in stable areas, while burial responsive mobile-dune plants are limited to areas of low vegetation height. This stem tissue density tradeoff was suggested as the mechanism determining the zonation that species show within the dune vegetation gradient present at various sites in South Africa. Finally, detailed investigations of dune plant ecophysiology found that: 1) The resources used in the response to burial derive from external sources of carbon and nitrogen, as well as simple physiological and physical mechanisms of resource allocation. 2) The leaves of dune plants were found to be operating at one extreme of the photosynthetic continuum; viz efficient use of leaf nitrogen at the expense of water loss. 3) Contrary to other ecosystems, the environmental characteristics of dunes may allow plants to occupy a high disturbance, high stress niche, through the maintenance of lowered competition. 4) At least two mobile-dune species form steep dunes, and are able to optimise growth, on steeper dunes, such that they have to grow less in response to burial than plants that form more shallow dunes. In this thesis, it was shown that the link between the carbon and nitrogen economies of dune plants was pivotal in determining species distributions and survival under extreme environmental conditions. As vast areas of the world’s surface are covered by sand dunes these observations are not just of passing interest.

Thesis (MSc (Botany and Zoology))--Unkiversity of Stellenbosch, 2009.
Phylogeographic genetic structure has been documented for a number of southern African terrestrial taxa. Information regarding geographic population genetic structuring in multiple taxa, with differing life histories, can provide insights into abiotic processes such as vicariance. A fragment of the cytochrome b mitochondrial DNA gene of a plains-dwelling species, Otomys unisulcatus, was sequenced and analysed. Two closely related geographic assemblages were found. The first assemblage (lowland group) contains populations from both the eastern and western parts of the species range, and the second comprises populations from the Little Karoo (central group). The lowland group was shown to be in a state of population expansion after a relatively recent mitochondrial DNA (mtDNA) coalescence, while the genetic signature of the central assemblage was characterized by more genetic diversity indicative of an older lineage/genetic refuge. Areas of higher elevation (namely mountain ranges) appeared to be the main factor limiting gene flow between these two groups. Aridification cycles due to glacial maximum periods probably resulted in increased dispersal leading to the widespread distribution of common haplotypes throughout the lowland group. Morphological variation in skull shape and size has been shown to follow environmental clines in some rodents. Geometric morphometric analyses on the ventral and dorsal views of the craniums of O. unisulcatus were utilised to test whether the population groupings obtained in the genetic analyses would be recovered by morphometric analyses. In addition, it was also investigated which of the environmental factors investigated influenced skull shape and size. The genetic groupings were not recovered for either the cranial shape or size. Size variation in the females correlated positively with annual rainfall, and so by proxy with habitat productivity, indicating that females which inhabited areas with lower rainfall would be larger. The significant relationship between females’ centroid sizes and rainfall was thought to be as a result of the increased nutrient requirement by this gender in the production of offspring. The males did not show a significant correlation between any of the environmental variables and centroid size. There was a significant difference between the skull shapes of the genders, further verifying the sexual dimorphism in the species. Three major clusters were found (according to cranium shape) using a Two-Block Partial Least Squares Analysis (2B-PLS), which relate to the biome boundaries within the species’ range. Variations in shape were attributed to the varying needs for strong masticatory muscles resulting from differing diets. The skull shapes of specimens occurring along the escarpment were intermediate between the first two clusters. Cranial shape in the male dorsal view dataset was significantly correlated with the environmental variables block, possibly due to the much lower minimum temperature in the Sutherland population (a population which was not included in the female analyses). It was concluded that differing diets of individuals in the respective biomes influenced the shape of the cranium of both genders. The sexual dimorphism in the cranium shapes may be as a result of the females digging tunnels (using their teeth) underneath the stick nests. Otomys unisulcatus show high levels of phenotypic plasticity throughout the range and it thus appears that the species can adapt fast to the different environmental variables.

Thesis (MSc)--University of Stellenbosch, 2005.
ENGLISH ABSTRACT:This study concentrates on the Bontebok (Damaliscus pygargus pygargus Pallas 1766) population of the Bontebok National Park. Using a combination of literature research, field observations, satellite imagery, Geographic Information System mapping and dung analysis, their habitat preferences within the Park are ascertained and compared to different behavioural and environmental factors. Considering vegetation composition and height, grass cover, burning history, general topography, water availability, actual diet quality (from faecal analysis) and population distribution, the best predictor of spatial pattern are investigated with GIS Dempster-Shafer models. The historical density distribution of the animals in the Park can be used to predict sustainable stocking rates. As far as possible, the results for the Bontebok are compared to those of the other larger herbivores in Bontebok National Park i.e. Red Hartebeest, Cape Mountain Zebra and Grey Rhebuck. These results should be useful for Wildlife Managers to know how to manage veld for Bontebok and at what stocking rates this can be done sustainably.
AFRIKAANSE OPSOMMING: Hierdie studie fokus op die Bontebok (Damaliscus pygargus pygargus, Pallas 1766) bevolking van die Bontebok Nasionale Park. Deur ‘n kombinasie van literatuurstudie, veldobservasies, satlietbeelde, Geografiese Inligtingstelsel (GIS) kartering en mis-analise te gebruik, word Bontebok habitatvoorkeure in die Park vasgestel en met verskillende gedrags- en omgewingsfaktore vergelyk. Deur te kyk na plantegroei-samestelling en hoogte, grasbedekking, brandgeskiedenis, algemene topografie, water-beskikbaarheid, diëet kwaliteit en die Bontebokke se waargenome ruimtelike verspreiding, word die faktor wat die verspreidingspatroon die beste voorspel, m.b.v. GIS Dempster-Shafer modelle ondersoek. Die historiese digtheidsverspreiding van diere in die Park word gebruik om volhoubare veldladings te voorspel. Sover moontlik word die resultate vir Bontebok vergelyk.met die ander groter herbivore in die Bontebok Nasionale Park, te wete Rooi Hartebees, Kaapse Bergsebra en Vaalribbok. Hierdie resultate behoort vir Natuurlewe-bestuurders tot nut te wees as riglyne vir veldbestuur en volhoubare veldladings van Bontebok.

Narrow riparian woodlands along non-perennial streams have made it possible for vervet monkeys to penetrate the semi-arid karoo ecosystem of South Africa, while artificial water points have more recently allowed these populations to colonize much more marginal habitat away from natural water sources. In order to determine the sequelae of life in these narrow, linear woodlands for historically 'natural' populations, I determined the size of troops in relation to their reliance on natural and artificial water sources and collected detailed data from two river-centred troops on activity, diet and ranging behaviour over an annual cycle. These data indicate that river-centred troops were distinctive primarily for their large group sizes and, consequently, their large adult cohorts, and the extent of home range overlap in what is regarded as a territorial species. While large group size carried the corollary of increased day journey length and longer estimated interbirth intervals, there was little other indication of ecological stress. Specifically, the rate of predation appears to be lower than observed at other sites. Predation encounters here, encourage the use of predator vigilance rather than influencing the use of space within the habitat. The high density of Acacia karoo, which accounted for a third of annual foraging effort in what was a relatively depauperate floristic habitat, allows for an adequate energy intake for groups of this size. I ascribed the large group size and home range overlap to the inability of groups to undergo fission.
xiii, 79 leaves : ill., maps ; 29 cm

Water temperatures are a fundamental water quality component, and a key abiotic determinant of fish distribution patterns in rivers. A river 's thermal regime is the product of a multitude of thermal drivers and buffers interacting at different temporal and spatial scales, including, inter alia, air temperatures, flow volumes (including groundwater flows and lateral inputs from tributaries), channel geomorphology and riparian vegetation. "Healthy" river systems are self-sustaining, with adequate thermal variability to maintain biotic diversity. Temporal variability of flow volumes and water temperatures, and how these change along the longitudinal axis of a river, contribute towards a rivers "signature". Rivers that have had their signatures altered through anthropogenic impacts may no longer be sustainable, and require varying levels of management. Successful river management should include a quantification of these signatures , a definition of the "desired" state which management aims to achieve, associated "thresholds" of change or concern, and monitoring programmes. Such an approach requires flexibility and adaptability, as well as appropriate tools being available to natural resource managers. Indices, the utility of which are enhanced when included in predicative modelling systems, are a common means of assessing system variability and change. The degree of confidence placed in such tools depends on the level of fundamental science, and the degree of system understanding, underpinning them. This research contributes to the understanding of the ecological significance . of water temperatures in variable semi-arid river systems, using the Sabie River (Mpumalanga, South Africa) as a case study, and indices derived from biological indicators (Chiloglanis , Pisces: Mochokidae) to quantify the effects of cumulative changes in heat units against a hypothesised critical water temperature threshold. Hourly water temperatures for 20002002 collected at nine sites in the main rivers of the Sabie catchment, together with biannual surveys of relative abundances and community patterns of fish collected using standard electrofishing techniques, were used to provide the basis for a modelling system which aims to provide river managers with a tool for quantifying changes to the thermal regime of the Sabie River. This modelling system consisted of a suite of pragmatic models, including multiple linear regression models for simulating daily maximum water temperatures, and simple cause-and-effect relationships between biological indices (change In condition factor and change in the ratio of relative abundances of two species of Chiloglanis) and annual metrics of time-of-exposure to heat stress. It was concluded that changes in the thermal regimes of the rivers in the Sabie catchment are likely to lead to changes in fish distribution patterns, and a decline in river health. Inherent system variability suggests that management decisions will be made in the face considerable uncertainty. Indirect management of water temperatures may be possible through maintenance of flow volumes and flow variability. However, the most appropriate management approach for maintaining fish diversity within these rivers is to ensure that obstacles to fish migration are minimized, to maximise the ability of river biota to respond to thermal changes, by accessing suitable alternative habitats or refugia. Future research should focus on extending the time series of water temperatures from such river systems, and further understanding the drivers and buffers contributing to the thermal regimes of variable semi-arid river systems in South Africa. Additional testing of the validity of the hypothesized relationships between abiotic processes underpinning biotic patterns should be undertaken.
Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 2003.

Range change is a common species response to global change. Comparing historical species distribution data with recent biological surveys has the potential to quantify changes to species geographic ranges. However, the broad-scale sampling strategies typically employed to acquire primary species distribution data are prone to errors of omission. The aim of this study was to evaluate the South African Frog Atlas Project (SAFAP) as a means for detecting changes in amphibian species distributions and to relate observed range changes to extrinsic environmental factors and intrinsic species characteristics. The SAFAP provided historical (1905 – 1995) and recent (1996 – 2003) species distributions of the amphibians of South Africa. Geographic sampling bias in the dataset was assessed by relating collection density and species richness to hypothesised sources of bias. Several methods for managing differing sampling intensity were tested on hypothetical ranges. The best methods were applied to the South African species to investigate range dynamics. Changes to the size of species ranges and shifts in mean range centre were assessed. An Ecological Niche Factor Analysis provided comparative measures of climate and habitat niche breadth for each species. SAFAP sampling was concentrated around cities, roads and protected areas, resulting in relatively overestimated species richness and range sizes near to these features. Large parts of the arid northwestern regions were under-sampled. An increase in sampling intensity over time resulted in the false detection of range expansions. The most reliable method to correct for increased sampling was a mathematical correction factor, according to which, 60.2% of South African frog species have undergone range contractions. Upslope shifts of 47.6 m were found for South African species and species of the Bushveld region shifted towards an area of Savanna Biome resilience. While several of the observed changes to species ranges were consistent with global change predictions, southern hemisphere amphibians may show a differing response to global change to that which is commonly predicted. Small range size, habitat specialisation and climate specialisation were significant predictors of range contractions for all species. Contracting habitat specialists were concentrated within two areas of endemism that also had high levels of land transformation. The use of methods that correct for sampling variation has allowed the SAFAP to be valuable in investigating species range change.

Thesis (MTech. Nature Conservaion) -- Tshwane University of Technology 2013.
The aim of this study was to determine the current population status of Aloe peglerae in the Magaliesberg Mountain Range.

Metabolomics is a discipline where metabolites are assessed, identified and quantified in different samples. Metabolites are crucial components of the biological system and highly informative about its functional state due to the closeness to functional endpoints and to the organism’s phenotypes. 1H NMR and LC-MS, the commonly used metabolomics analytical platforms were used to annotate the metabolites found in Sclerocarya birrea (S. birrea) leaves from five South African provinces, Limpopo (L), Gauteng (G), North West (NW), Mpumalanga (M) and KwaZulu-Natal (KZN). Supervised Orthogonal Partial Least Square – Discriminant Analysis (OPLS-DA) of the full spectra revealed a clear differentiation of S. birrea leaves from five provinces. In addition, the level of common metabolites were measured and compounds previously found to have anti-diabetes potential ((-)-epicatechin 3-0-galloyl ester, myricetin-3-0-α-L-rhamnopyranoside, gallic acid and Kaempferol-3-0-α-L-rhamnopyranoside) were annotated in the samples. The samples from the five provinces showed anti- diabetic activity when exposed to an in-vitro glucose uptake assay, with the highest activity observed in male samples from M. The sample presented high concentrations of (-)-epicathechin 3-0-galloyl ester, one of the metabolites with anti-diabetes activity. Overall 1H NMR and LC-MS metabolic profiling were successfully applied to discriminate all five sources of S. birrea leaves, and obtained qualitative information of many common metabolites
Agriculture, Animal Health and Human Ecology
M. Sc. (Agriculture)

Rhipicephalus microplus belongs to the Ixodidae, the largest family of ticks, which are of great economic importance due to their negative socio-economic impact on agriculture (BROUQUI 2011; PORTO NETOA et al. 2011; SONENSHINE 1991). Acaricides have been the first choice in tick control for cattle farmers, but R. microplus rapidly acquires resistance to these chemicals. Replication slippage and recombination drive genetic diversity in tick populations (BAFFI et al. 2007; GUERRERO et al. 2007; LI et al. 2007); generating point mutations and frame shifts within the genes targeted by acaricides, resulting in resistance (BAFFI et al. 2007; HERNANDEZ et al. 2002; HERNANDEZ et al. 2000; JONSSON et al. 2010; MORGAN et al. 2009). In addition, resistance can quickly accumulate in a population due to the pangamy mating structure of ticks (CHEVILLON et al. 2007b; CUTULLÉ et al. 2010) and their ability to produce multiple generations within one season (BUDELI et al. 2009; LI et al. 2007). Vaccines have become increasingly important to control ticks, as acaricide resistance can be acquired by field tick populations within two years (RODRIGUEZ-VIVAS et al. 2011). Although Bm86 has been successful against multiple-acaricide resistant ticks, recent reports indicate that the Bm86 vaccine has become ineffective, possibly due to resistance (PARIZI et al. 2009). Also, Bm86 vaccines display great variability in terms of their efficacy against ticks isolated across Argentina (GARCIA-GARCIA et al. 2000; PARIZI et al. 2009). This is hypothesised to be due to the genetic variability between R. micoplus populations. The majority of phylogenetic studies on ticks have been based on slow evolving sequences, such as 18S or 28S rRNA, which provide genus-level resolution. The COI, D3, ANT and ITS2 genes have the potential to resolve intra-specific and interspecies variation, and may assist with the identification of cryptic speciation within R. microplus of South Africa (ANSTEAD et al. 2011; BARKER 1998; CAREW et al. 2009; MURRELL et al. 2000; SONGA et al. 2011). Phylogeography is a multidisciplinary field that utilises phylogenetic (molecular evidence of speciation) and population genetic principles (coalescence theory), in combination with additional data (such as geography and population history), to determine the genetic relationships of populations within a species (AVISE 2009) and was one of the main aspects of this study. The phylogenetic and population genetic structure of R. microplus will provide valuable information to geneticists, farmers and acaricide/vaccine suppliers about the different R. microplus tick populations of South Africa. The information will facilitate more efficient and targeted tick control whether acaricide or vaccine based as opposed to the inefficient approaches generally adopted to tick control.
Dissertation (MSc)--University of Pretoria, 2014.
lk2014
Genetics
MSc
Unrestricted

A major challenge in savanna rangeland studies is estimating woody vegetation cover and densities over large areas where field based census alone is impractical. It is therefore crucial that the management and conservation oriented research in savannas identify data sources that provides quick, timely and economical means to obtain information on vegetation cover. Satellite remote sensing can provide such information. Remote sensing investigations, however, require establishing statistical relationships between field and remotely sensed data. Usually regression is the empirical method applied to field and remotely sensed data for the spatial estimation of woody vegetation variables. Geostatistical techniques, which take spatial autocorrelation of variables into consideration, have rarely been used for this purpose. We investigated the possibility of improving woody biomass predictions in tropical savannas using cokriging. Cokriging was used to evaluate the cross-correlated information between SPOT (Satellites Pour l’Observation de la Terre or Earth-observing Satellites)-derived vegetation variables and field sampled woody vegetation percentage canopy cover and density. The main focus was to estimate woody density and map the distribution of woody cover in an African savanna environment. In order to select the best SPOT-derived vegetation variable that best correlate with field sampled woody variables, several spectral vegetation and texture indices were evaluated. Next, variogram models were developed: one for woody canopy cover and density, one for the best SPOT-derived vegetation variable, and a crossvariogram between woody variables and best SPOT-derived data. These variograms were then used in cokriging to estimate woody density and map its spatial distribution. Results obtained indicate that through cokriging, the estimation accuracy can be improved compared to ordinary kriging and stepwise linear regression. Cokriging therefore provided a method to combine field and remotely sensed data to accurately estimate woody cover variables.
Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.

M.Sc. (Botany)
In South Africa, controlling and eradicating Azolla filiculoides and Eichhornia crassipes cost annually approximately US$ 60 million to the national budget. However, the success of these operations is mixed because invasive aquatic plants often spread very rapidly either before they are spotted or before decisions are taken to implement control actions. This limitation is further exacerbated by difficulties in determining the invasion potential of newly introduced or unknown aquatic plants, as well as difficulties inherent to species identification. Resolving these drawbacks requires pre-emptive actions such as identifying areas that are most vulnerable to invasion by alien plants. In this study, I first explore whether molecular technique such as DNA barcoding can be useful to: i) overcome potential limitation of morphology-based identification of invasive aquatic plants; and ii) establish successful control of these invasives. For this purpose, I tested the utility of official DNA barcodes (rbcLa + matK or core barcodes), trnH-psbA, and the core barcode + trnH-psbA to identify invasive aquatic plants of South Africa’s freshwaters. Second, I use the technique of ecological niche modeling to identify most vulnerable freshwater systems to species invasion under current and climatic conditions. My analysis indicates that the core barcodes and matK regions perform poorer compared to trnH-psbA, which provides 100% successful identification alone or in combination with the core barcodes. This study therefore validates trnH-psbA as single best DNA barcode for invasive alien aquatic plants of freshwater systems in South Africa. Using this DNA region in BLAST analysis to screen plants species sold in aquarium market in Johannesburg, I found surprisingly that some prohibited species are already in circulation in the market. These include Hydrilla verticillata, egeria densa, Myriophyllum spicatum, and Echinodorus cordifolius. Furthermore, based on climatic parameters, I explored the distribution of the "bad five" aquatic species in South Africa, i.e. the most damaging invaders of freshwater systems. I found distinct distribution potentials for these species under current climatic conditions. Overall, 38% of all South Africa’s dams occur in areas climatically vulnerable to the invasion by the bad five with the Western Cape Province being the most vulnerable. However, under predicted climate change scenario, I found evidence for contrasting shifts in species range: species such as Azolla filiculoides, Eichhornia crassipes, Salvinia molesta might increase their range by at most 2% whilst the ranges of Myriophyllum aquaticum and Pistia stratiotes might contract by at most 5%. This range contraction and expansion will result in some dams currently vulnerable to invasion becoming resilient whilst others that are currently resilient might become vulnerable owing to climate change. This result demonstrates not only the utility of DNA barcoding in implementing control measures, but also provides ways of prioritising control/management efforts.

Since the earliest reported cases of HIV/AIDS probably in 1959 in Africa, there has been a consistent progression in the new HIV/AIDS infection cases. In South Africa, Gauteng, records one of the highest HIV/AIDS prevalence rates in the country. The Department of Health (DOH) South Africa conducts ongoing studies on HIV/AIDS at provincial levels; these studies monitor the prevalence of HIV/AIDS amongst pregnant women attending antenatal clinics, as a tool for determining and monitoring the prevalence, trends, patterns and spread of the disease in the general population. This study analyses sentinel and spatial data collected from the (DOH) and Statistics South Africa (StatsSA) respectively, and depicts them in the form of spatial maps, and then critically analyses the spatial patterns that occur. The research findings would hopefully contribute to the overall knowledge of HIV/AIDS and provide framework and relevant literature for further investigation.
Geography
M.Sc. (Geography)

Fire plays an important role in structuring and maintaining savanna grassland ecosystems. Although regular fires are a characteristic feature of savannas, the effects of fire frequency on these systems are less well known, particularly with respect to how frequency of fire influences large herbivore distribution and behaviour. The expectation is that large herbivores should be attracted to frequently burned sites as a consequence of changes in forage quality and quantity, and/or vegetation structure and composition. The former could be driven by alterations in soil nutrients, such as N and P. Alterations in vegetation also could be important in determining risk of predation. For example, an increase in woody vegetation could decrease predator visibility making large herbivores more vulnerable to predation. The objectives of this study were to investigate the effects of long-term alterations in fire frequency on herbivore distribution and behaviour, as well as the mechanisms (soil nutrients, vegetation structure and composition, and forage quality and quantity) potentially driving the distribution of large herbivores. To address these objectives, I conducted large herbivore surveys on a bi-weekly basis from 2009-2010 in a series of plots in the Experimental Burn Plots (EBPs) burnt at different frequencies (annual, triennial and unburnt) over the last five decades at three study sites in the Kruger National Park, South Africa. Surveys also were conducted on new plots that were established adjacent to the long-term plots. These new plots have a fire return interval of 4 years which is similar to the triennially burned plots of the EBPs. They were established in the landscape adjacent to the EBPs to assess whether the responses of herbivores to fire observed in the EBPs reflected was at landscape level. The distribution of all large herbivore species combined and of grazers (e.g. zebra) or browsers (e.g. kudu) only were not affected by fire frequency. In contrast, the abundance of mixed-feeders, such as impala, was significantly higher in the unburnt (control) and annually burned plots than the triennially burned plots. Although season did not have a significant impact on the distribution of browsers and mixed-feeders, overall more grazers were recorded across all burn treatments in the dry season compared to the wet season. Similar patterns of herbivore distribution were observed between the new plots and the triennially burned EBP plots, suggesting that responses observed to the long-term fire frequency treatments reflects herbivore responses at the landscape level. The long-term fire frequency treatments significantly affected soil nutrients (N, organic C, P, and K were significantly lower with annual burning), vegetation structure (abundance of woody plants were greater in unburned plots), and forage quantity (unburned plots had higher biomass) but not quality. More frequent fires improved visibility by reducing tree height and density and herbaceous biomass, thereby potentially reducing predation risk, when compared to less frequent burning. As a result, herbivores selected sites with more frequent fires. The behaviour of the herbivore species investigated was predominantly influenced by seasonal-induced changes to their environment rather than fire frequency. In the wet season irrespective of the burning treatment visibility was low due to high rainfall that increases plant biomass, whereas in the dry season visibility was improved because there is little to no rainfall. This potential alteration in predation risk likely resulted in herbivores being more vigilant in the wet season than the dry season. Overall, results from this study suggest that the combination of fire frequency and season drive herbivore distribution and behaviour by altering mainly the vegetation structure which can influence predation risk.
Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

Parthenium hysterophorus (Asteraceae), classified as an emerging weed in South Africa, has become abundant throughout large parts of southern and eastern Africa. In South Africa it has invaded areas in KwaZulu-Natal, Mpumalanga, the North West Province and Limpopo. A biological control programme against parthenium weed was launched in South Africa in 2003, based on the success achieved in Australia. Zygogramma bicolorata, a leaf-feeding beetle native to Mexico, was imported into South Africa via Central Queensland, Australia where it was released in the 1980s. This thesis examines aspects of the thermal physiology of Z. bicolorata which, in conjunction with its native and exotic geographical distribution, was used to predict the potential distribution of the agent in South Africa, in relation to climate. To determine Z. bicolorata’s physiological capability, several physiological parameters were examined for mechanistic modelling purposes. These parameters included the beetle’s lethal thermal limits, critical thermal limits, lethal humidities (Chapter 2) and developmental rate at constant temperatures (Chapter 3). In Chapter 4, these physiological parameters were entered into the dynamic modelling program CLIMEX (CLIMEX programme ver. 2, CSIRO Entomology ©) and a map of the areas that are acceptable for the establishment of Z. bicolorata was produced. The CLIMEX model predicted that most of South Africa is favourable for the establishment of the beetle, except in the west of the country and in the north of Lesotho, extending into South Africa. All areas in which parthenium currently occurs were predicted to be very favourable for Z. bicolorata establishment and proliferation. Optimal release sites aimed at initial establishment were earmarked at three areas in the northeastern part of South Africa (Jozini, Ndumu Game Reserve and along the road from Swaziland to Mozambique). It is concluded that Z. bicolorata is climatically suited to South Africa, increasing the likelihood that populations will establish and proliferate when released.
Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.

The biology of the Grey-headed Gull was studied between 2004 and 2005 in South Africa's Gauteng, KwaZulu-Natal and Northern Cape provinces. Grey-headed Gulls have a widespread but patchy distribution in South Africa, occurring both inland and at the coast. Their largest population is centred on Gauteng, where the species appears to be a relatively recent colonizer and where the current breeding population is estimated at 2185 breeding pairs (the largest in South Africa). There is evidence that the species has also increased in other parts of South Africa, especially at Port Elizabeth in the Eastern Cape. The majority of coastal birds are found in KwaZulu-Natal and there is strong evidence for regular movements of adult birds between Durban and Lake St Lucia. By contrast, little evidence was found for a putative large-scale, regular movement between Gauteng and KwaZulu-Natal. The breeding biology of the Grey-headed Gull was studied at four sites in Gauteng and at Lake St Lucia's Lane Island during 2004 and 2005. The distance between the Gauteng sites ranges from 1.7 km, between Lakefield Pan and Korsman's Bird Sanctuary, to 25.3 km, between Bonaero Park and Modderfontein Pan. The approximate distance between Gauteng and Lake St Lucia is 460 km. The mean clutch size at all sites was 2.42 eggs and the mean incubation period was 24.9 days. Parental investment in incubation was approximately equal between the sexes while males spent more time in attendance and participated in more aggressive encounters. Empirical growth curves are given for mass, wing, culmen, head and foot morphometrics of Grey-headed Gull chicks. Intraspecific variation in breeding parameters reveal significant differences between sites, including: highly synchronous laying at Lake St Lucia; the largest eggs and fastest growing chicks at Gauteng's Modderfontein Pan (a small, peripheral colony); and the smallest eggs and slowest growing chicks at Gauteng's Lakefield Pan (a large, 'core' colony). Possible reasons for these differences include the relative localities of each site in terms of feeding opportunities, high levels of predation by African Fish Eagle's at Lane Island, and density dependent factors operating on the large colonies within the core population on Gauteng's East Rand. Overall daily egg survival was comparatively high for all sites in Gauteng and low for Lane Island nests. Morphometric, plumage and bare-parts data from a sample of trapped and resighted birds are used to age, sex and determine the timing and duration of moult in the Greyheaded Gull. Six age classes were identified and, for all measurements, males were significantly larger than females. The mean duration of primary moult was 136 days between October and January and there were two waves of secondary moult.
Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

This dissertation undertakes an analysis of the spatial persistence of population in South Africa over the period 1911 to 2011. A comprehensive review is given of the history and development of geographical economics in order to understand the dynamics of the forces of agglomeration. In addition the history of the development of South Africa is discussed and special focus is directed to the geographical, economic and political factors that gave rise to the unequal distribution of population and wealth in the country. In the empirical analysis Zipf’s law was applied and it was found that South Africa’s population was more evenly spread in 1911. With the application of the law to the 2011 data the Pareto exponent of the OLS log-linear regression indicated that urban agglomeration was more persistent. Although this might indicate that apartheid did not influence agglomeration in South Africa it is argued that the nature of the agglomeration was in fact influenced by restrictive measures placed on the urbanisation of the population and industrial decentralisation policies. It is indicated that the apartheid policy altered the equilibrium spatial distribution of population and wealth which lead to a smaller than optimal primate and second largest magisterial districts, too many secondary cities of similar size, and also too many small and uneconomical rural settlements.
MCom (Economics), North-West University, Potchefstroom Campus, 2015

Morphological-taxonomical study of gryporhynchid cestodes from Africa is presented. New material from Kenya, Senegal and Sudan was studied and we belong to 17 species in 8 orders - Amirthalingamia macracantha (Joyeux et Baer, 1935) Bray, 1974; Anomotaenia riccii (Fuhrmann et Baer, 1943) Baer et Bona, 1960; Cyclustera magna (Baer, 1959) Bona, 1975; Cyclustera sp.; Dendrouterina macrosphincter (Fuhrmann, 1909) Baer et Bona, 1960; Neogryporhynchus sp.; Paradilepis lloydi (Southwell, 1926) Spasski, 1954; Paradilepis maleki (Khalil, 1961); Paradilepis urceina Bona, 1975; Paradilepis urceus (Wedl, 1855) Joyeux et Baer, 1950; Parvitaenia macrocoleo Bona, 1975; Parvitaenia macropeos (Wedl, 1855) Baer et Bona, 1960; Parvitaenia megascolecina Bona, 1975; Parvitaenia purpurea Johri, 1959; Parvitaenia samfyia Mettrick, 1967; Valipora ardeolae (Singh, 1952) Baer et Bona, 1960 and Valipora mutabilis (Linton, 1927). Known larval stages and adults from Africa are presented in review of species.