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.