abstract: The Cape Floral Region (CFR) in southwestern South Africa is one of the most diverse in the world, with >9,000 plant species, 70% of which are endemic, in an area of only ~90,000 km2. Many have suggested that the CFR's heterogeneous environment, with respect to landscape gradients, vegetation, rainfall, elevation, and soil fertility, is responsible for the origin and maintenance of this biodiversity. While studies have struggled to link species diversity with these features, no study has attempted to associate patterns of gene flow with environmental data to determine how CFR biodiversity evolves on different scales. Here, a molecular population genetic data is presented for a widespread CFR plant, Leucadendron salignum, across 51 locations with 5-kb of chloroplast (cpDNA) and 6-kb of unlinked nuclear (nuDNA) DNA sequences in a dataset of 305 individuals. In the cpDNA dataset, significant genetic structure was found to vary on temporal and spatial scales, separating Western and Eastern Capes - the latter of which appears to be recently derived from the former - with the highest diversity in the heart of the CFR in a central region. A second study applied a statistical model using vegetation and soil composition and found fine-scale genetic divergence is better explained by this landscape resistance model than a geographic distance model. Finally, a third analysis contrasted cpDNA and nuDNA datasets, and revealed very little geographic structure in the latter, suggesting that seed and pollen dispersal can have different evolutionary genetic histories of gene flow on even small CFR scales. These three studies together caution that different genomic markers need to be considered when modeling the geographic and temporal origin of CFR groups. From a greater perspective, the results here are consistent with the hypothesis that landscape heterogeneity is one driving influence in limiting gene flow across the CFR that can lead to species diversity on fine-scales. Nonetheless, while this pattern may be true of the widespread L. salignum, the extension of this approach is now warranted for other CFR species with varying ranges and dispersal mechanisms to determine how universal these patterns of landscape genetic diversity are. / Dissertation/Thesis / Ph.D. Biology 2013

Philosophiae Doctor - PhD / Moss frogs are restricted to permanently moist terrestrial habitats in the south-western Cape Fold Mountains. There is a very close association between Arthroleptella distribution and Table Mountain Sandstone. Suitable habitats are generally occupied by allopatric populations of moss frogs. Comprehensive spatial sampling of moss frogs (genus Arthroleptella) in the Cape Floristic Region biodiversity hotspot yielded 192 new distribution records; 5 842 advertisement calls from 240 individual male frogs; 31 Rag-1,76 16S, 54 12S sequences and morphological measurements of 90 specimens. There are many differences in male advertisement call and genetic sequences between populations on different mountain ranges, even over small distances. A mitochondrial and nuclear gene phylogeny of the southern African Pyxicephalidae places Natalobatrachus as the sister genus to Arthroleptella. Application of a Bayesian relaxed molecular clock model indicates that Arthroleptella arose between 20 and 39 Ma. Phylogenetic trees return two main clades within Arthroleptella: one consists of species which exhibit chirp-like calls and the second contains species with longer calls composed of a series of clicks. These two clades diverged between 19 and 22 Ma. There is a general pattern of strong phylogeographic structure with many small, isolated populations. Three species are identified within the Chirping clade and seven in the Clicking clade, including three undescribed species. This population structure is a result of the patchy distribution of suitable habitat and low vagility of the moss frogs.The distribution and speciation of moss frogs has been affected by drying and cooling climate change, changing geomorphology over the last 20 Ma and the increasing prevalence of fire over the last 5 Ma. An assessment of the threat status of each species according to IUCN criteria categorised one species as Least Concern, seven as Near Threatened, one as Vulnerable and one as Critically Endangered. The primary threats to Arthroleptella are invasive alien plants and increased fire frequencies and intensities.