Thesis (MSc (Botany and Zoology))--Stellenbosch University, 2011. / ENGLISH ABSTRACT: The comparative phylogeography of the host-parasite relationship of the southern African endemic dark shyshark, Haploblepharus pictus and its nematode parasite, Proleptus obtusus was investigated. To date, no studies have been conducted on the population structure of catsharks and their species specific parasites and little is known about the population dynamics of these species. A total of 116 catsharks and 201 parasites were analysed from seven South African localities. The mitochondrial marker COI was used and species specific primers were designed for both the host and parasite. Haplotype networks were constructed and no strong geographically structured groupings were found for either species. Pairwise st values for the parasite and host found Gansbaai to be significantly differentiated from the other sites. Fu’s Fs were significantly negative for both host and parasite indicating population disequilibrium. Proleptus obtusus displayed a pattern of population expansion which was confirmed by the mismatch distribution. Mismatch distributions failed to indicate population expansion for the sharks. Other factors such as selection, migration or genetic drift are likely the cause of the population disequilibrium detected. Interestingly, no barrier to gene flow was found around Cape Point, a known break for other species such as the clinid, Clinus cottoides and the caridean shrimp Palaemon peringueyi. The outcome of this study suggests that levels of gene flow in H. pictus are high enough to suggest that the documented site fidelity is not as strong as originally proposed. The parasite, being dependent on the host, shows a similarly high level of gene flow among sampling sites. / AFRIKAANSE OPSOMMING: Die vergelykende filogeografie van die gasheer-parasiet verhouding tussen die endemiese suider-Afrikaanse donker skaamhaai, Haploblepharus pictus en sy nematode parasiet, Proleptus obtusus is ondersoek. Huidiglik is daar nog geen ander studies uitgevoer met betrekking tot die populasie struktuur van skaamhaaie en hul spesies-spesefieke parasiete nie en min is bekend oor die populasie dinamiek van hierdie spesies. In hierdies studie is ‘n totaal van 116 skaamhaaie en 201 parasiete vanaf sewe lokaliteite geanaliseer. Die mitikondriale merker COI is hiervoor gebruik en spesie spesefieke inleiers is vir beide gasheer en parasiet ontwerp. Haplotipe netwerke is saamgestel vir beide spesies en het geen duidelike geografies gestruktureerde groepe aangedui nie. Paarsgewyse st waardes van beide parasiet en gasheer het daarop gedui dat Gansbaai geneties gedifferensieerd is van alle ander lokaliteite. Fu se Fs was statisties betekenisvol met ‘n negatiewe waarde vir beide spesies, wat dui op populasie disekwilibrium. Proleptus obtusus het ‘n patroon van populasie groei getoon, wat deur Fu se Fs en die misparing verspreiding bevestig is. Die misparing verspreiding het nie populasie toename vir die skaamhaaie aangedui nie. Die waargeneemde populasie disekwilibrium is waarskynlik die gevolg van seleksie, migrasie of genetiese drywing. Geen genetiese breuk is by Kaap Punt, wat ‘n genetiese breuk vir verskeie ander spesies soos Clinus cottoides en Palaemon peringueyi is, gevind nie. Die uitkomstes van hierdie studie stel voor dat vlakke van geen vloei in H. picuts hoog genoeg is om ‘n patroon van genetiese vermenging tussen lokaliteite, op die mitokondriale DNS vlak, tot gevolg te hê. Dit beteken moontlik dat die gedokumenteerde gebied gebondenheid van hierdie spesie nie so sterk, soos oorspronklik voorgestel, is nie. Die parasiet, waarskynlik aangesien hy van sy gasheer afhanklik is, toon ‘n soortgelyke hoë vlak van geen vloei tussen lokaliteite. Dus toon beide spesies ‘n algehele afwesigheid van genetiese struktuur, met die isolasie van Gansbaai van alle ander lokaliteite.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Human-modified habitats form increasingly large components of landscapes, threatening biodiversity and creating challenges for conservation. In some cases altered habitats form entirely novel ecosystems that may support new combinations of species and species abundances, and create habitat space in otherwise transformed landscapes. In the Western Cape of South Africa, woody invasive species contribute to landscape-level habitat transformation and form novel ecosystems. Invasive Australian Acacia species are especially problematic in lowland areas where they create dense thickets and substantially transform both biotic communities and abiotic processes. Despite the prominence of Acacia thickets across the Western Cape, their ability to support native fauna is not well understood and the objective of this study was to assess the significance of Acacia thickets as habitat for the region’s avifauna. Birds were surveyed in Acacia thickets in the south-western Western Cape in three seasons to examine species richness, abundance and functional abundance. Furthermore, I examined the extent to which differences in patch-level vegetation structure alter bird communities. Between survey sites and seasons, significant variation was observed in assemblage richness, density, median body size and biomass. Variation in vegetation density, stem density, mean vegetation height and total canopy cover best explained variation in bird assemblages. Eighty species were estimated to utilize Acacia thickets and assemblages had a mean density of 7.78 birds per ha. The most abundant feeding guilds were the mixed feeders and insectivores. The median body size observed was 15.2 g and the body size frequency distribution of all species in Acacia spanned a similar range compared to the body size frequency distribution for the species list for the entire Western Cape. The mean biomass of bird communities was 0.224 kg per ha. Using data on bird density and biomass, Acacia thickets across the Fynbos Biome support and estimated average of over 21 million birds with a combined biomass of over 600 thousand kg. This study found that Acacia thickets in the Western Cape support a subset of the region’s birds with the most abundant species being small mixed feeders, which are also frequently urban-adapted. Compared with other habitat types, Acacia support bird assemblages with moderate species richness and density. This study shows that Acacia thickets, as a novel habitat, provide a significant amount of habitat space in a highly transformed landscape and highlights the need for comprehensive evaluation of altered habitats before assumptions are made about their ecological value. / AFRIKAANSE OPSOMMING: Getransformeerde habitatte maak vermeerderend groot deel uit van die omgewing, dit bedreig biodiversiteit en skep groter uitdagings vir bewaring. In sommige gevalle vorm hierdie getransformeerde habitatte geheel nuwe ekosisteme wat moontlik nuwe kombinasies van spesies en spesie volopheid kan onderhou. Verder skep nuwe ekosisteme habitat spasie in anders veranderde landskappe. In die Wes-Kaap van Suid-Afrika dra die Australiese Acacia indringer spesies is veral problematies in laagliggende areas, aangesien dit digte ruigtes vorm, asook beide die biotiese gemeenskappe en die abiotiese prosesse aansienlik transformeer. Ten spyte daarvan dat daar volop Acacia ruigtes in die WesKaap is, word min verstaan van hul vermoë om inheemse fauna te onderhou. Die hoofdoel van hierdie studie was om die belang van Acacia ruigtes as habitat vir die area se voëllewe te bepaal. Voël-opnames in die suidwestelike dele van die Wes-Kaap is gedoen in Acacia ruigtes oor drie seisoene, om spesierykheid, volopheid en funksionele volopheid te ondersoek. Verder is die mate waartoe verskille in die plotte van die plantegroei struktuur, die voëlgemeenskappe verander, geondersoek. Daar was aansienlike variasie waargeneem in die spesiesamestelling rykheid, voorkoms digtheid, mediaan liggaamsgrootte en biomassa van die voëls tussen die onderskeie voëlopnaam plotte en die seisoene. Die variasie in plantegroei digtheid, stam digtheid, mediaan plantegroeihoogte en totale kroonbedekking verduidelik hierdie variasie in spesiesamestelling die beste. Tagtig voëlspesies Acacia ruigtes benut en die populasiesamestelling het ‘n gemiddelde digtheid van 7,78 voëls per ha. Die mees algemene voel-voeding-guldes was die gemengde-voedsel-vreters en insekvreters. Die median liggaamsgrootte waargeneem was 15,2 g en die liggaamsgrootte frekwensieverspreiding van alle spesies in Acacia ruigtes is ooreenkomstig met die liggaamsgrootte frekwensieverspreiding vir die spesielys vir die hele Wes-Kaap. Die gemiddelde biomassa van voel gemeenskappe was 0.224 kg per ha. Acacia ruigtes oor die fynbosbioom wat ‘n geskatte gemiddelde van meer as 21 miljoen voels ondersteun, met ‘n gesamentlike biomassa van meer as 600 duisend kg. Hierdie studie het bevind dat Acacia ruigtes in die Wes-Kaap ‘n onderafdeling van die streek se voels ondersteun, met die mees algemene spesies as die klein gemengde-voedsel-vreters, wat ook dikwels stedelik aangepas is. In vergelyking met ander habitattipes ondersteun Acacia ruigtes voel samestellings met matige spesierykheid en digtheid. Hierdie studie toon dat die Acacia ruigtes, as ‘n nuwe habitat, ‘n beduidende hoeveelheid habitat ruimte in ‘n hoogs getransformeerde omgewing skep en beklemtoon die behoefte aan ‘n omvattende evaluering van veranderde habitatte, voor aannames gemaak word oor hul ekologiese waarde.

Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: The aim of this study was to investigate the phylogeographic structuring of the honey badger, Mellivora capensis, a highly mobile medium sized carnivore with an extensive distribution throughout sub-Saharan Africa extending into the Middle East and India. Particular focus was placed on providing preliminary data potentially useful for the development of translocation policies for this species in southern Africa. Where possible, genetic results were also compared with current trinomial designations to determine whether subspecies status given to geographical groupings was supported by the genetic data. Mitochondrial control region sequence data was obtained for most a selection of specimen’s available while nuclear microsatellite variation was determined for a subset of individuals where there were sufficient sample sizes available. Phylogeographic structuring of the maternal mitochondrial lineage was initially obscured by the coamplification of a closely related numt. To overcome co-amplification, the numt was identified and mtDNA specific primers were designed. Mitochondrial DNA results are based on the most variable 230 bp of the control region (sequenced for 78 individuals) while five polymorphic nuclear microsatellite markers were scored (for 55 individuals). Analysis, employing both nuclear and mitochondrial data, showed that although a pattern of isolation by distance can be detected, there was evidence for the presence of phylogeographic structuring between eastern and southern Africa. This could be interpreted as due to vicariance, probably associated by rifting and climatic occilations during the Pleistocene. Analyses support the identification of distinct management units for eastern and southern African populations although some evidence exists for secondary introgression between these two regions. Following this, we recommend that translocations between these broad geographic areas should be avoided. Within these geographic areas, because of a general pattern of isolation by distance, we recommend that individuals for translocations come from geographically proximate populations. In some instances, phylogeographic structuring is concordant with subspecies designations but additional sampling will be needed to make any firm taxonomic conclusions. / AFRIKAANSE OPSOMMING: Die doelwit van hierdie studie was om die filogeografiese struktuur van die ratel, Mellivora capensis, ‘n hoogs bewegende medium groot karnivoor met ‘n wydverspreide distribusie deur sub-Sahara Afrika wat strek tot in die Midde Ooste en India, te bepaal. Spesifieke fokus is geplaas op die voorsiening van preliminêre data potensieel bruikbaar vir dir ontwikkeling van verplasing strategieë vir hierdie spesie in suidelike Afrika. Genetiese resultate is, waar moontlik, vergelyk met huidige drieledige kategorieë om te bepaal of subspesies ondersteun word deur die genetiese data. Mitochondriale ‘control region’ DNS volgorde data was verkry vir die meeste van die monsters beskikbaar en kern mikrosatelliet variasie was bepaal vir ‘n gedeelte van individue waar voldoende monster groottes beskikbaar was. Filogeografiese strukturering van die materne mitochondriale merker was oorspronklik versteek deur die ko-amplifikasie van ‘n naby verwante ‘numt’. Om die ko-amplifikasie te oorkom is die ‘numt’ geïdentifiseer en mtDNS spesifieke voorvoerders is ontwerp. Mitochondriale DNS resultate is gebaseer op die mees veranderlike 230 bp van die ‘control region’ (waar die DNS volgorde vir 78 individue bepaal is) en vyf polimorfiese kern mikrosatelliet merkers (in 55 individue). Analises, wat gebruik maak van kern en mitochondriale data, toon wel ‘n patroon van isolasie deur afstand, maar ook ‘n duidelike sigbare filogeograpfiese strukturering tussen oostelike en suidelike Afrika. Hierdie is geïnterpreteer as vikariansie, heel waarskynlik ge-assosieer deur berg verskuiwings en klimaatsveranderinge deur die Pleistocene. Analises ondersteun die identifikasie van definitiewe verkillende bestuurseenhede vir oostelike en suidelike Afrika maar sekere bewyse bestaan dat sekondêre introgressie tussen streke bestaan. Dit word aanbeveel dat translokasies tussen hierdie geografiese areas voorkom moet word. Binne geografiese areas, as gevolg van ‘n algemene patroon van isolasie deur afstand, is dit aanbeveel dat individue vir verplasing van nabygeleë populasies moet wees. In sommige gevalle het filogeografiese strukturering ooreen gestem met subspesies kategorieë, maar verdere materiaal is nodig voor definitiewe taksonomiese besluite geneem kan word.

Thesis (MSc)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: This study investigated the evolution of the genus Palinurus at the higher and lower taxonomic levels. The population genetics of the spiny lobster, Palinurus delagoae, was investigated by making use of a portion of the mitochondrial DNA (mtDNA) control region (547 base pairs) that was sequenced for 285 lobsters from the southeastern coast of Africa (six sites) and 49 lobsters from Walters Shoals (one site), a submerged seamount on the Madagascar Ridge. Lobsters from these two areas shared no haplotypes and differed by at least 27 mutational steps. An analysis of molecular variance showed significant genetic partitioning, and pairwise comparisons suggested that lobsters from Walters Shoals are distinct from those of other sampling areas. Along the south east African coastline there was shallow genetic partitioning between four southern sites (South Africa) and two northern (Mozambique) sites, suggesting two Management Units along the African coast. Female gene flow along the African coast may be propagated by larval dispersal in the Mozambique and Agulhas Currents and counter-current migrations by benthic juveniles along the shelf, but the mtDNA data strongly suggest that larvae at Walters Shoals have been, or are currently still retained by other oceanographic processes. The magnitude of mtDNA divergence among lobsters from the southeastern coast of Africa and those at Walters Shoals, together with the absence of any shared haplotypes between these regions, strongly suggested that these two taxa represent distinct species. The molecular data of the large subunit ribosomal RNA, 16S rRNA (481 bp), and cytochrome oxidase subunit I, COI (520 bp) were then used for a higher level phylogenetic analysis of the genus. A total of 33 individuals (five representatives from each of the six species), and two outgroups (Projasus parkeri and Palinustus unicornutus), were subjected to maximum parsimony, maximum likelihood and Bayesian inference analyses. All analyses were conducted on both the separate data sets as well as a combination of the two genes. Bootstrap analyses of the 16S rRNA data resulted in >70% support for the monophyly of all six Palinurus species but no support could be obtained for any of the interspecific associations. Likewise, individual analyses of the COI gene resulted in strong support for the monophyly of the species. The combined data (parsimony analyses) increased the resolution considerably and apart from the monophyly of all six species, good bootstrap support was also obtained for associations among species. The topology for the maximum likelihood analyses displayed a more resolved and well supported tree when the basal ingroup taxon P. elephas was used to root the tree. The combined Bayesian analyses did not result in a well resolved topology and no significant posterior probabilities could be obtained reflecting the associations among species. / AFRIKAANSE OPSOMMING: Hierdie studie het die evolusie van die genus Palinurus by hoë en laer taksonomiese vlakke ondersoek. Die bevolkingsgenetika studie op die kreef, Palinurus delagoae, is ondersoek deur gebruik te maak van 'n gedeelte van die mitokondriale (mtDNA) kontrole-area (547 basispare) waarvan die volgorde bepaal is vir 285 krewe van die suidoos-kus van Afrika (afkomstig van ses verskillende gebiede) en 49 krewe afkomstig van Walters Shoals (een gebied), 'n ondersese berg op die Madagaskar Rand. Krewe van hierdie twee areas deel geen haplotipes nie en verskil met ten minste 27 mutasiestappe. 'n Analise van die molekulêre variansie toon dat daar 'n beduidende genetiese verdeling tussen die twee groepe is en 'n gepaarde vergelyking toon dat krewe afkomstig van Walters Shoals verskil beduidend van krewe uit ander gebiede. Volgens die vlak genetiese verdeling tussen die vier suidelike (Suid-Afrika) en twee noordelike (Mosambiek) gebiede van die suidoos-kus van Afrika wil dit voorkom of daar twee bestuurseenhede langs die kuslyn van Afrika is. Vroulike geenvloei langs hierdie kuslyn kan dalk bevarder word deur larwale verspreiding in die Mosambiek- en Agulhas- Seestrome en teenstroom migrasie van jong bodemwonende krefies op die kontinentale plaat. Die mtDNA data stel egter voor dat kreeflarwes by Walters Shoals deur ander oseanografiese prosesse steeds (of tot onlangs toe) behou word. Die grootte van mtDNA divergering tussen krewe van die suidoos-kus van Afrika en die by Walters Shoals, sowel as die afwesigheid van enige gemeenskaplike haplotipes tussen die twee gebiede, toon met beduidende sekerheid aan dat hierdie twee taksa twee unieke spesies verteenwoordig. Die molekulêre data van die 16S-rRNA (481bp) van die groot ribosomale-subeenheid en die sitochroom oksidase subeenheid, COI (520bp) is gebruik om 'n hoër resolusie filogenetiese analise van die genus te bepaal. Data van 33 individue (vyf individue uit elk van die ses spesies) en twee buitegroepe (Projasnus parkeri en Palinustus uniconutus) is geanaliseer deur gebruik te maak van die maksimum-parsimonie, die maksimum-waarskynlikheid en die Bayes-inferensie metodes. Alle analises is uitgevoer op beide die afsonderlike datastelle sowel as op die gekombineerde data van die twee gene. Analise van die 16S-rRNA data deur die skoenlusmetode (steekproefhersteekproef- metode) toon meer as 70% steun vir die monofilie van al ses Palinurus spesies maar dit toon geen steun vir enige van die interspesifieke assosiasies nie. Net so toon individuele analise van die COI geen beduidende steun vir die monofilie van die spesies. Die gekombineerde data (parsimonie) het 'n aansienlike verhoging in die resolusie teweeg gebring en behalwe vir die monofilie van al ses die spesies was daar ook goeie steun deur die skoenlusmetode vir die assosiasie tussen spesies verkry. Die topologie vir die maksimum-parsimonie het 'n goed gesteunde en hoër resolusie boom vir die gekombineerde datastel (sonder die buitegroepe) getoon. Die gekombineerde Bayesanalise het nie 'n soortgelyke boom opgelewer nie en die assosiasie tussen die spesies is nie ondersteun nie aangesien geen beduidende a posteriori-waarskynlikheid verkry kon word nie.

Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: The development of potential genetically based resistance to cadmium (Cd) after long-term exposure to this metal at a sublethal concentration, was investigated in earthworm specimens belonging to the genus Eisenia. Adult (clitellate) earthworms from a long-term laboratory Cdexposed population (> 78 generations) and from other populations having no previous history of metal exposure were exposed to increasing concentrations (0; 2.5; 5; 10 and 20 mg/l) of Cd in the form of CdSO4. Different biomarkers and molecular markers were used to determine whether the specimens from the long-term Cd-exposed population had acclimatized or adapted to the metal contaminated environment. Acclimation was investigated at different physiological and biochemical levels using the following three biomarkers: the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay (MTT assay) measuring mitochondrial activity and cell viability; the single cell gel electrophoresis assay (comet assay) measuring DNA strand breaks and the biosynthesis of metallothioneins (MTs) that have the function of lowering metal toxicity. Earthworms from the long-term exposed substrate as well as specimens from populations not exposed to Cd were used. Adaptation was investigated by looking at both allozyme polymorphism at seven enzyme encoding loci and DNA polymorphism using chosen neutral and selectable genetic markers. The markers used were cytochrome c oxydase subunit I (COI) and metallothionein-2 (mt-2) respectively. This was done amongst the same pool of populations. Additionally, the DNA polymorphism study also aimed at genetically identifying the species utilized in this study thereby determining whether these earthworms belong to the species Eisenia fetida or Eisenia andrei. MTs biosynthesis did not generate the expected data mainly due to the fact that a suitable antibody could not be obtained (discussed in Chapter 5 section 5.3.3.). Similarly, the assessment of DNA polymorphism at the chosen selectable genetic marker mt-2 did provide information relevant to understanding the potential development of resistance to Cd in the long-term metal contaminated group. COI sequences generated in this study were compared to E. fetida and E. andrei COI sequences available on Genbank. Consequently, specimens used in this study were identified as possibly belonging to the species E. andrei. Allozyme polymorphism revealed no fixed genetic differences between the long-term Cd exposed laboratory culture and the rest of the populations. All the populations departed from Hardy-Weinberg equilibrium (χ2 > 5.9; p < 0.05), and showed a low mean heterozygosity per locus (Ho ≤ 0.21), probably due to inbreeding. Cell viability and proliferation as tested by the MTT assay revealed that coelomocytes, isolated from the long-term Cd-exposed group showed the highest viability (98.42%) compared to those from other groups (+/- 80%). Kruskal-Wallis ANOVA (H2, 225=109.7165 p < 0.001) revealed that the long-term Cd-exposed laboratory culture showed a better response to acute exposure to Cd, thus demonstrating that these worms have developed some kind of tolerance to Cd. Similarly, the comet assay showed that in the long-term Cd-exposed specimens, less DNA breaks occurred after Cd exposure than in the unexposed groups. Of all the comet parameters assessed in this study (comet tail length, tail moment and tail DNA percentage), tail DNA percentage seemed to be more sensitive although all three parameters indicated that long-term Cd-exposed specimens were more resistant than unexposed specimens as shown by the number of single strand DNA breaks induced by exposure to higher concentrations of Cd (p < 0.001). The comet and the MTT assays indicated that the earthworms with a previous history of Cd exposure have developed increased fitness towards higher doses of Cd, compared to previously unexposed groups. These findings mainly proved that several mechanisms could come into play at the physiological and biochemical level to allow the Cd exposed population to acclimatize to its chemically stressful environment. Clear genetic support for the differences found between the tested populations was not obtained, but needs to be investigated further using Cd selectable markers such as the mt-2 gene, in order to come to a more conclusive deduction. / AFRIKAANSE OPSOMMING: Die moontlike ontwikkeling van geneties gebaseerde weerstand teen kadmium (Cd) by erdwurms van die genus Eisenia, na langtermyn blootstelling aan die metaal by 'n subletale konsentrasie, is ondersoek. Volwasse (klitellate) erdwurms van 'n langtermyn laboratorium Cdblootgestelde bevolking (< 78 generasies) asook van ander bevolkings met geen voorgeskiedenis van metaal blootstelling nie, is blootgestel aan 'n reeks van Cd konsentrasies (0; 2.5; 5; 10; en 20 mg/l) in die vorm van CdSO4. Verskillende biomerkers en molekulêre merkers is gebruik om vas te stel of die erdwurms geakklimeer of aangepas het by die metaal in die gekontamineerde omgewing. Akklimasie is op verskillende fisiologiese en biochemiese vlakke getoets deur die volgende drie biomerkers te gebruik: Die 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromied toets (MTT toets), wat mitochondriale aktiwiteit en sel lewensvatbaarheid meet; die enkel sel elektroforese toets (Komeettoets) wat DNS string breuke meet; die biosintese van metallotioniene (MT's) wat metaalvergiftiging verlaag. Erdwurms van die langtermyn blootstellingsubstraat asook eksemplare van bevolkings wat nie aan kadmium blootgestel was nie, is gebruik. Aanpassing is ondersoek deur gebruik te maak van allosiem polimorfisme, waar 7 ensiem koderende lokusse gebruik is asook van DNS polimorfisme deur neutrale genetiese merkers te selekteer. Die merkers wat gebruik is, was sitochroom c oksidase, subeenheid I (COI) en metallotionien-2 (mt-2) respektiwelik. Hierdie toetse is met dieselfde groepe bevolkings uitgevoer. 'n Bykomende van die studie aspek waar ook van DNS polimorfisme gebruik gemaak is, was daarop gemik om die spesie wat vir die huidige studie gebruik is, geneties te identifiseer en om vas te stel of die erdwurms aan die spesie Eisenia fetida of Eisenia andrei behoort. Die MT biosintese het nie die verwagte data gegenereer nie, hoofsaaklik weens die feit dat geskikte teenligaampies nie beskikbaar was nie (bespreek in Hoofstuk 5 afdeling 5.3.3). Soortgelyk, het die waardebepaling van DNS polimorfisme by die geselekteerde genetiese merker mt-2 nie genoegsame informasie verskaf om die potensiaal van die ontwikkeling van weerstand teen Cd in die langtermyn blootgestelde groep te verstaan nie. COI geenvolgordes van E. fetida en E. andrei wat op Genbank beskikbaar was, is gebruik om met die resultate van die huidige studie te vergelyk. Die spesie wat tydens die huidige studie gebruik is, is op hierdie wyse geïdentifiseer as E. andrei. Allosiem polimorfisme het geen vaste genetiese verskille tussen die langtermyn blootgestelde laboratoriumkulture en die ander bevolkings getoon nie. Al die bevolkings het verskil van die Hardy-Weinberg ewewigstoestand (χ2 > 5.9; p < 0.05) en het 'n lae heterosigositeit per lokus getoon (Ho ≤ 0.21), moontlik as gevolg van inteling. Sellewensvatbaarheid en proliferasie soos getoets met die MTT toets, het getoon dat selomosiete, geïsoleer vanuit die langtermyn Cd blootgestelde groep, die hoogste lewensvatbaarheid (98.42%) gehad het in vergelyking met die ander groepe (+/- 80%). Kruksal-Wallis ANOVA (H2, 225=109.7165 p < 0.001) het getoon dat die langtermyn Cd blootgestelde laboratoriumkultuur 'n beter respons vir akute blootstelling aan Cd gehad het. Hierdeur is gedemonstreer dat hierdie wurms 'n soort toleransie teenoor kadmium ontwikkel het. Soortgelyk het die komeettoets aangetoon dat daar in die langtermyn blootgestelde eksemplare minder DNS breuke voorgekom het na verdere blootstelling aan Cd as in die ander groepe. Van al die komeet parameters wat tydens die studie gemeet is (komeet stertlengte, Olive stert moment en stert DNS persentasie), het die stert DNS persentasie geblyk om die mees sensitiefste te wees, alhoewel al drie parameters aangetoon het dat die langtermyn Cd blootgestelde eksemplare meer weerstandbiedend was teen induksie van DNS enkelstring breuke weens Cd blootstelling (p < 0.001), as die wat nie voorheen blootgestel was nie. Die komeet en MTT toetse het aangetoon dat erdwurms met 'n voorgeskiedenis van Cd blootstelling 'n toenemende fiksheid teen hoër dososse van Cd ontwikkel het as die wat nie voorheen aan kadmium blootgestel was nie. My bevindings kon hoofsaaklik toon dat verskeie meganismes op die fisiologiese en biochemiese vlak 'n rol sou kon speel om Cd blootgestelde bevolkings by 'n chemies stresvolle omgewing te laat akklimeer. Duidelike ondersteuning vir die verskille tussen die getoetsde bevolkings deur van Cd geselekteerde merkers soos die mt-2 geen gebruik te maak om 'n meer finale afleiding te kan maak is nie verkry nie en behoort verder ondersoek te word.

Thesis (MSc (Botany and Zoology))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT:Chapter 1 - Mealybugs are tiny, soft-bodied insects which constitute the second largest scale insect family Pseudococcidae (Downie & Gullan 2004). The family comprises approximately 2000 species in 300 genera (Ben-Dov 1994), of which 20 species are pests of cultivated plants in South Africa (Annecke & Moran 1982). In South Africa, approximately 109 species of mealybugs have been recorded from 50 genera (Millar 2002). Chapter 2 - The effect of constant temperatures on the development, survival and fecundity of the oleander mealybug, Paracoccus burnerae on citrus was determined. Developmental time, rate of development, fecundity and survival were investigated at five constant temperatures and a 16L: 8D light: darkness regime. The rate of development increased linearly with an increase in temperature for the egg, 1st nymphal and pupal stages as well as the entire biological cycle (egg – adult), but was nonlinear for the 2nd and 3rd nymphal stages. Survival decreased with an increase in temperature. P. burnerae required 666.7 degree-days above a lower threshold of 8.7°C to complete one generation. The highest mean number of 68 eggs per female was reached at 22°C. A sex ratio of 0.52:0.48 (male:female) was obtained from the life table. The net reproductive rate (Ro) was >1 at all five temperatures, an indication that it is capable of increasing its population numbers despite the high mortality experienced in the 1st and 2nd nymphal stages. Chapter 3 - The oleander mealybug, Paracoccus burnerae (Brain) is a pest of citrus in South Africa. This study was carried out to determine the effect of temperature on development rate of P. burnerae and to investigate whether development rate is the reason why P. burnerae is out competing the citrus mealybug, Planococcus citri (Risso), in the Eastern and Western Cape Provinces of South Africa. The influence of temperature on life history traits of P. burnerae was determined at 20, 22, 25 and 27°C and compared with corresponding data for P. citri. The rate of development increased linearly with an increase in rearing temperature in the embryonic, first nymphal and pupal stages but reached a climax at 26.13 and 28.6°C in the second nymphal stage of both species, respectively. P. citri exhibited lower developmental thresholds except in first instar, shorter degree-days and higher developmental rates than P. burnerae. Results of the current study indicated that the dominance of oleander mealybug over the citrus mealybug is neither linked to developmental rates nor sum of effective temperatures. Chapter 4 - The importance of Paracoccus burnerae has risen over the years to an extent where it is now regarded as a quarantine pest for citrus fruit from South Africa. The field biology of P. burnerae on citrus in the Western Cape Province of South Africa was studied through periodic sampling of leaves from twigs enclosed in sleeve cages. The species composition and abundance of natural enemies was investigated. Both adult and immature stages attained maximum population peaks in March and P. burnerae had four generations. The highest level of mortality was experienced in the immature stages. Climate and an unidentified fungus were the key mortality factors. The level of abundance of the two observed predators, the harlequin beetle, Harmonia axyridis and the green lacewing, Chrysoperla sp. was relatively low. Although parasitism occurred in some cages, the level was low ranging between 1.62 to 9.43%. If biocontrol is the preferred method of controlling P. burnerae, suitable candidate parasitoids for inoculative biocontrol are Acerophagus sp., Leptomastix sp. and Microterys nietneri. The oleander mealybug does not share the same parasitoids with Planococcus citri, Pseudococcus calceolariae and Pseudococcus longispinus except the parasitoid Coccophagus sp. The most popular species of parasitoids used in the biolological control of mealybugs, Anagyrus sp. and Coccixenoides sp. were insignificant in the case of P. burnerae. Chapetr 5 - Biological control programs of mealybug species have relied on sprouting potatoes, pumpkins and butternut for rearing of both mealybugs and their natural enemies. In this study, the suitability of sprouting potatoes, butternuts and citrus as mass rearing substrates for the oleander mealybug, Paracoccus burnerae was investigated. Developmental times, rate and fecundity on each substrate were determined and compared at three different temperatures. The developmental time on sprouting potatoes was shorter than on citrus. P. burnerae was unable to complete its life cycle on butternut. The rate of development increased linearly with an increase in temperature on both sprouting potatoes and citrus. P. burnerae required 666.7 degree-days on citrus and 434.8 degree-days on sprouting potatoes above lower developmental thresholds of 7.6°C and 10.4°C respectively to complete one generation. The mean number of eggs per female was higher on sprouting potatoes (121.3) than on citrus (68), but declined with an increase in temperature from 22 to 27°C. Despite the shorter shelf life, sprouting potatoes are the preferred host for mass rearing of the oleander mealybug. Chapter 6 - general conclusions Chapter 7 - Researchers often present impressive results of their studies on the biology of the Coccoidea without mentioning the problems they came across and had to solve. In this paper the practical problems encountered during a study of the biology of the oleander mealybug, Paracoccus burnerae (Brain), an endemic pest of citrus in South Africa, are discussed. / AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.

Thesis (MSc)--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: This study examines the phylogeography of the southern African vlei rat, Otomys irroratus using the mtDNA cyt b gene and chromosomal data derived using G-, and C-banding, Ag-NOR staining and fluorescence in situ hybridization (FISH using flow sorts of Myotomys unisulcatus). A total of N = 102 specimens were used from the Western Cape, Eastern Cape, Northern Cape, Free State, Mpumalanga and KwaZulu-Natal provinces of South Africa. Of the N = 102, N = 55 comprised fresh material while N = 47 comprises museum material obtained from the Durban Natural Science Museum of South Africa. Cytogentic analysis of N = 55 specimens collected from seven localities in South Africa revealed intra-specific variation resulting from two rearrangements, namely pericentric inversions and heterochromatin variation. Of the 55 specimens that were analyzed 47% contained inversions or centromeric shifts on four autosomes (OIR1, OIR4, OIR6 and OIR10) which were present singly in specimens (i.e. none of the specimens contained all four inversions concurrently). These inversions were present in both homozygous and heterozygous state over a wide geographic range suggesting that they are floating polymorphisms. Given the potential role of inversions in post-mating isolation (through production of aneuploid gametes), the prevalence of inversions as floating polymorphisms in the vlei rats suggest that they are probably retained in the population through suppression of recombination in the inverted regions of the chromosomes. In addition, differences between populations is due to the presence or absence of heterochromatic arms (and not inversions), which cause variation in the NFa (40 – 49) and supernumerary B chromosomes, resulting in the variation in diploid number (2n = 28 – 32). Analysis of N = 55 specimens revealed Ag-NORs on 7 autosomal pairs 1, 2, 5, 7, 8 and 9 proximal to the centromere on the short arm of the chromosome. Pair 8 also displayed Ag-NOR at the distal end of the long arm of the chromosome in individuals from the Free State province. Pair 3 showed two Ag- NORs occurring proximal to the centromere on the short arm and on the terminal end of the long arm, respectively. I obtained 953bp of mtDNA cyt b from fresh material and 400bp from museum material. Using maximum parsimony and Bayesian inference two main clades were retrieved. Clade A specimens occur mainly in the Western and Eastern Cape provinces of South Africa. Clade B specimens occur in the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape and Mpumalanga provinces of South Africa. The mean sequence divergence between the main clades (A and B) is 7.0% and between sub-clades comprising clade B is 4.8%, while within clade A the sequence divergence was 1.91%. Nested clade analysis revealed allopatric fragmentation within O. irroratus. Chromosomal characters also support the two evolutionary lineages as clade A has pericentric inversions which occur as floating polymorphisms which are absent in clade B. Clade B in turn is fixed for a complex tandem fusion rearrangement which is absent from clade A. Divergence date estimates indicate that the two clades separated around 1.1 MYA, which coincides with climate changes since the late Pliocene/Pleistocene epochs. Cladogenesis within this species complex could therefore have been influenced by habitat fragmentation. A full taxonomic review of O. irroratus is therefore warranted by this study. / AFRIKAANSE OPSOMMING: Die suider Afrikaanse vlei rot, Otomys irroratus word gekenmerk deur fenotipiese konservatisme regoor die spesie se verspreiding en het groot chromosomale variasie met diploied chromosoom getalle wat reeks vanaf 2n = 23 tot 2n = 32. Hierdie variasie binne O. irroratus het gelei tot die beskrywing van drie chromosomale groupe naamlik die A sitotipe wat gekenmerk word deur 'n akrosentriese komplement. Die tweede groep wat die B sitotipe genoem word besit ten minste agt chromosoom pare met heterokromatiese kort arms, onderwyl die derde group (die C sitotipe) vier chromosoom pare het met heterokromatiese kort arms. Hierdie studie bestudeer die bevolkings genetika struktuur van O. irroratus deur 102 monsters te analiseer wat gekollekteer was regoor die spesie se verspreiding binne Suid-Afrika en die mitochondriale merker sitokroom b sowel as chromosoom fluoressent hibridisasie te gebruik. Ek het 55 monsters van sewe lokaliteite binne Suid-Afrika sitogeneties geanaliseer deur gebruik te maak van G- en C-bandbepaling asook die hibridisasie patrone geproduseer deur die vloeisorteerde chromosoome van Myotomys unisulcatus. Die analise het gewys dat 47% van die monsters perisentromeriese inversies besit het, wat slegs aangetref was of die outosome OIR1, OIR4, OIR6 en OIR10. Hierdie inversies was nooit almal teenwoordig binne dieselfde monster nie en was gevind in beide heterosigotiese en homosigotiese vorm. Die inversies kom ook voor oor 'n wye verspreiding wat daarop aandui dat dit swerwende polymorfisme is. Omdat inversies lei tot die produksie van aneuploiede gamete speel hulle 'n belangrike rol in post-parings reproduktiewe isolasie, die verskyning van swerwende inversies binne vlei rotte dui dus daarop dat hulle onderhou word binne populasie verband deur die onderdrukking van rekombinasie in die gedeeltes van die chromosoom. Verdere verskille tussen populasies behels die voorkoms of afwesigheid van heterochromatiese kort arms wat (nie inversies) wat lei tot die variasies in die Nfa (40 – 49). Die variasie in diploied getal (2n = 28 – 32) is eksklusief as gevolg van B chromosoome. Ag-NOR banding het ook gewys dat daar twee evolusionêre lyne binne O. irroratus voorkom. Verder het filogenetiese analise van al die monsters verkryg deur volgorde-bepaling met behulp van maksimale parsimonie en Bayesian afleiding twee klades geidentifiseer. Klade A diere kom voor in die Wes en Oos-Kaap provinsies van Suid-Afrika terwyl klade B diere voorkom in die Oos-Kaap, Vrystaat, KwaZulu-Natal, Noord-Kaap en Mpumalanga provinsies onderskeidelik van Suid-Afrika. Die gemiddelde volgorde-bepalings verskille beloop 7% tussen die twee hoof klades (A en B) en tussen sub-klades 4.8%, terwyl binne klade A die verskille slegs 1.91% beloop het. Analise van die verwantskap tussen die klades het gewys dat allopatriese fragmentasie heel waarskynlik gelei het tot die populasie genetiese struktuur binne O. irroratus. Chromosoom karakters onderskraag die twee evolusionêre lyne waar klade A slegs perisentriese inversies besit wat swerwend wat ontbreek in klade B. Klade B op sy beurt besit 'n komplekse tandemme fusie wat glad nie voorkom in klade A nie. Molekulêre datering het verder gewys dat die twee klades omtrent 1.1 miljoen jaar gelede versprei het, wat ooreenstem met die klimaats veranderinge wat sedert die Peioceen en Pleistoceen plaasgevind het. Klade vorming binne die spesies komples kan daarom as gevolg van habitat fragmentasie plaasgevind het. Hierdie studie dus noodsaak 'n volle taksonomiese ondersoek van O. irroratus ten einde vas te stel hoeveel spesies binne die komplex voorkom.

Thesis (MSc)--Stellenbosch University, 1985. / The gross morphology and histology of the alimentary canal and the associated structures are described. The long tubular alimentary tract is divisible into different regions. The filter chamber and Malpighian tubules are absent. The peritrophic membrane is also absent. The rectum, or hindgut is extremely thin, expanded and transparent. The salivary gland complex consists of two sets of glands: the principal and accessory glands. The common salivary duct opens at the base of the maxillary stylets.

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: South Africa's coastline is in the region of 3650kms and encompasses many different and dynamic marine environments. To enhance our current understanding of the population structure and gene flow patterns of intertidal zone marine species in this region, this study sets out to investigate the phylogeographic population structure of the Cape sea urchin, Parechinus angulosus, using mitochondrial and nuclear DNA sequence data collected in 2007 and 2008. Individuals were sampled from 18 geographic locations between southern Namibia and Durban, covering nearly the full extent of the species range. Sequence data were obtained from a 790bp region of the COI mtDNA gene (n=510) and a 182bp region of the nDNA SpREJ9 gene (n=145), respectively. The mtDNA data revealed 283 polymorphic sites (36%) defining 195 haplotypes, of which 160 were unique and 35 shared among individuals. Haplotype diversity (h) was found to be high both overall (h=0.95) and for individual localities (h=0.75-0.98), with nucleotide diversity (π) being low overall (π=0.013) as well as for individual localities (π=0.0033-0.0254). AMOVA revealed significant population structure among sampling sites in the Namaqua Province biogeographical region, as well as between three of the four respective coastal biogeographic provinces/regions. Gene flow was bi-directional among sampling sites in the south coast Agulhas and East Coast Province biogeographical regions, while gene flow in the Namaqua Province appears to be dominated by northwards movement. BAPS identified a significant break in the Cape Point region, which was also reflected in the gene flow patterns and parsimony networks. This broadly corresponds to previously identified biogeographic regions as well as genetic breaks for other marine species found along this coast. Fu's Fs statistics showed strong signal(s) of population expansion for individual sampling localities as well as for the data set as a whole, while MDIV estimated a time since expansion ranging from 7733-4759 years ago. The nDNA data revealed 54 variable sites (29.7%), defining 72 alleles of which 50 were unique and 22 shared among individuals. Many of the alleles (69.4%) were restricted to single sampling sites, with Betty's Bay on the south coast being the most diverse from a genetic viewpoint. Allelic diversity was high overall (h=0.86) while nucleotide diversity was low (π=0.025). No nuclear sub-group structure was identified by BAPS, although the parsimony network revealed shallow genetic structure between the Namaqua and Agulhas Provinces, with significant pairwise ФST values also recovered between their individual coastal localities. This points to at least one major barrier to gene flow for Parechinus angulosus along the South African coast, namely Cape Point. Several additional, smaller hindrances to gene flow along the coast were also identified, most of which are congruent with findings from studies on both other and sea urchin species. As a standalone study this research elucidated many aspects regarding the phylogeography of the Cape sea urchin, P. angulosus. However, it is when viewed in the broader context of invertebrate phylogeography along the southern African coastline that this research will provide its most critical insight. / AFRIKAANSE OPSOMMING: Geen opsomming

Thesis (MSc)--Stellenbosch University, 1998 / Stellenbosch University. Faculty of Science. Dept. of Botany & Zoology. / ENGLISH ABSTRACT: There has been a long-standing need to systematically analyze and classify South African fossil Lacertilia. Although extensive assemblages of fossil lizard and amphibian material from Langebaan on the West Coast and elsewhere exist in museum collections, the fragmentary nature of the material has largely prevented in-depth analyses and identification. In this comparative study the skulls and lower jaws of 7 lizard genera, representing the six extant South African families, were disassembled and the bones analyzed individually. The aim was to compile a comparative database of each bone against which current and future fossil finds could be matched. Detailed descriptions of the isolated elements were given. The results showed that despite some intra-generic variation, unique structural differences do exist in individual bones which may be utilized in the taxonomic assessment of fragmentary fossil material. / AFRIKAANSE OPSOMMING: Daar bestaan lank reeds 'n behoefte vir die sistematiese analise en klassifisering van fossielmateriaal van Suid-Afrikaanse Lacertilia. Alhoewel uitgebreide versamelings van akkedis- en amfibier-fossiele van Langebaan aan die Weskus en elders in museums bestaan, het die fragmentariese aard van die materiaal grootliks diepgaande analises en identifikasie belemmer In hierdie vergelykende studie is die skedels en onderkake van 7 akkedisgenera, wat die ses resente Suid-Afrikaanse families verteenwoordig, gedisartikuleer en elke been individueel geanaliseer. Die doel was om 'n vergelykende databasis van elke been saam te stel waarmee huidige en toekomstige fossielvondse vergelyk kan word. Gedetaileerde beskrywings van die ge'isoleerde elemente word gegee. Die resultate toon dat desondanks 'n mate van intra-generiese variasie, unieke strukturele verskille tussen individuele bene weI bestaan en dat hierdie verskille gebruik kan word om fossielfragmente taksonomies te analiseer.