Phylogeographic mitochondrial DNA (mtDNA) population structure was determined for Aethomys namaquensis and A. ineptus from southern Africa and Swaziland. It was evident from the study that A. namaquensis reflected a pattern of phylogenetic discontinuity with and without spatial separation between populations. Previously documented mtDNA phylogeographic patterns recorded in the rock hyrax, Procavia capensis and the red rock rabbit species, Pronolagus rupestris and P. randensis, coincided with the phylogeographic break that was detected in one of the mtDNA lineages (C) within A. namaquensis. Similar vicariant events may have been responsible for shaping evolutionary processes in the independent Procavia, Pronolagus and Aethomys lineages. In contrast, A. ineptus showed a pattern of shallow phylogeographic structuring. The marked genetic differences detected in A. namaquensis and A. ineptus may reflect the influences of habitat specificity, its fragmentation and the effects of life history on mtDNA gene flow. The study also revealed three genetically well-supported lineages within A. namaquensis: a lineage (A) found in the Limpopo valley, a lineage (B) widely distributed across the Karoo and a lineage (C) found across the grasslands of the North-West, Limpopo and Mpumalanga Provinces. These spatial distributions broadly coincided with the ranges of four previously proposed morphologically defined subspecies. From the present sample sizes, there is only good support, from a molecular point of view, for the subspecies A. n. lehocla (lineage B). In addition to the three well-supported lineages, six geographically restricted lineages were identified that could not be assigned to any of the four previously proposed subspecies, A. n. namaquensis, A. n. monticularis, A. n. alborarius and A. n. lehocla. Molecular techniques, specifically the analysis of the mtDNA cytochrome b gene, have been useful in the identification of sibling species. This technique has also proved to be useful in the identification of two cryptic species, A. chrysophilus and A. ineptus in this study. Phylogenetic analysis revealed two maternal groups corresponding to A. chrysophilus and A. ineptus. Distributional data of these two species, suggest that A. chrysophilus occupies the low elevations of the Limpopo River drainage, while A. ineptus occupies the remainder of South Africa at higher elevations, but expands into lower elevations in the southern portion of its range. Phylogenetic relationships among four southern African species of Aethomys suggest the presence of two clades that included: 1) A. chrysophilus and A. ineptus and 2) A. namaquensis and A. granti. This study, however, revealed that Aethomys may be paraphyletic, suggesting that the allocation of A. namaquensis and A. granti to the subgenus Micaelamys needs to be investigated further. / Dissertation (MSc (Genetics))--University of Pretoria, 2006. / Genetics / unrestricted

Instability characterizes the taxonomy of the African rodent subfamily Otomyinae. Two genera, Otomys and Parotomys, and 14 species are currently recognized, but the generic subdivision is equivocal. Between two and five cytotypes are delimited within O. irroratus, which illustrate a rapid rate of karyotypic evolution, and may reflect incipient speciation. In an attempt to resolve the group's phylogeny, the mitochondrial cyt b (complete) and 12S rRNA (802 bp) genes were analyzed using parsimony, distance and maximum likelihood methods. Alternative models of evolutionary change were compared to determine the best-fit model for each data set. Both genes failed to resolve deeper evolutionary associations, but the cyt b gene proved useful in resolving relationships among closely related taxa. Robust associations consistently retrieved include: (1) the O. irroratus cytotypes form a monophyletic group with O. laminatus basal. (2) an exclusively East African clade comprises two representatives of O. anchietae lacustris (not sister taxa), O. tropicalis with O. denti basal~ (3) Otomys angoniensis and O. maximus from southern Africa are monophyletic sister taxa with O. typus jacksoni and O. typus successively basal, making the East African Otomyinae non-monophyletic. (4) Parotomys brantsii and P. Wtledalei cluster within Otomys, but with no clear sister relationships. These results question some of the nomenclatural divisions in current use. First, the paraphyly of Otomys renders the recognition of two distinct genera unsupported. Second, the strongly supported monophyletic clustering of O. angoniensis and O. maximus coupled with the comparatively small genetic distance separating them, disputes the status of O. maximus. Third, the paraphyletic associations shown for representatives of O. typus and O. anchietae might imply that distinct evolutionary lineages are contained within these species. Otomys irroratus is phylogenetically distant from other Otomys species previously considered conspecifics. Moreover, a sister association between the Band C cytotypes to the exclusion of Al and A2, corroborate the delimitation of two major cytogenetic groups within O. irroratus. The major clades form an unresolved polytomy suggesting that the Otomyinae experienced a rapid radiation approximately 5 Myr ago. A biogeographical scenario is presented in light of palaeo-climatic changes during the late Miocene and Plio-Pleistocene epochs. / Thesis (DPhil (Zoology))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted