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

Xylose is an unusual nectar sugar found in the nectar of Protea and Faurea (Proteaceae). Since nectar composition is an important floral characteristic in plant strategies for ensuring reproductive success, the unexplained presence of xylose in Protea nectar prompted this study of the interaction between pollinators and Protea species. Among pollinators that visit Proteaflowers in the south-western Cape Floral Kingdom, South Africa, insects and birds show an aversion to, and are poor assimilators of, xylose, whereas rodents such as Namaqua rock mice Aethomys namaquensis are the only pollinators so far shown to consume xylose willingly, and are able to obtain metabolic energy from this sugar. Mammalian tissues are not capable of catabolizing xylose efficiently, but certain gastrointestinal microflora are, through a process of fermentation which produces short-chain fatty acids used by host animals in oxidative metabolism. I explored mechanisms enabling Aethomys namaquensis to utilize xylose, in particular, the role of resident intestinal microflora in this process. Chapter One discusses pollination syndromes and the definitions thereof, mammal pollination, with particular reference to Australia and South Africa, and explains the rationale behind the questions addressed in this thesis. To assess xylose utilization in wild-caught mice with and without their natural gastrointestinal microflora, an antibiotic treatment was developed (Chapter Two). The veterinary antimicrobial agent, Baytril 10% oral solution, was found to be effective in significantly reducing gut microflora in animals on a four-day treatment protocol. The protocol developed here reduced the gut microflora sufficiently for subsequent experiments comparing xylose utilization in mice with and without intact microflora. Xylose utilization was assessed using 14C-labelled xylose (Chapter Three). Rock mice were caught during Protea humifloraflowering and non-flowering seasons, and fed 14C-labelled xylose. Exhaled CO 2 and excreted urine and faeces were collected, and label recovery determined. These experiments showed that xylose-utilizing bacteria in the rock mouse gut are very important for xylose utilization. More efficient xylose utilization during the flowering season suggests that this component of the gut microflora is inducible. Culturable gut microflora were then isolated from rock mouse faecal and caecal samples, assessed for xylose utilization to identify positive xylose-fermenters and classified by 16S rRNA based taxonomy (Chapter Four). Faecal isolates were Lactobacillus murinus and Enterococcus faecium, and caecal isolates were three Bacillus species, Shigella boydii, one Arthrobacter species and two fungal isolates from Aspergillus and Penicillium genera. The types and concentrations of short-chain fatty acids arising from xylose fermentation by caecal microflora were measured using gas chromatography. The fatty acid profile produced by rock mouse gut microflora is similar to that for other animals that rely on gut microbial fermentation to produce fatty acids then used in oxidative metabolism. Chapter Five concludes with a discussion of possible explanations for the presence of xylose as a nectar sugar, its ecological significance, and the relevance of the fermentative capacity of pollinator digestive systems for xylose utilization in animals. / Thesis (PhD (Zoology))--University of Pretoria, 2007. / Zoology and Entomology / unrestricted