This thesis reports the results of a systematic investigation of the genus Bitis, Africa's most taxonomically diverse and geographically widespread genus of viperid snakes, in addition to phylogeographic investigations of its most geographically widespread representative, Bitis arietans. The phylogeny of Bitis is inferred using mitochondrial sequences plus those from two phylogenetically informative nuclear markers, and analysed using recently developed multispecies coalescent methods. These analyses successfully resolve the phylogenetic position of several rare and previously unstudied species and confirm the majority of intrageneric relationships. Several instances where current taxonomy may not adequately portray evolutionary relationships among these snakes are also revealed.
The development of five anonymous nuclear markers for the genus is also reported that will be valuable for future studies, and are utilised here in more focussed investigations of the puff adder, B. arietans. A pan-African phylogeographic investigation of B. arietans reveals the presence of multiple parapatric mitochondrial clades. The historical processes responsible for generating phylogeographic structure in southern Africa are investigated using species distribution modelling and genetic approaches, which support isolation in multiple southern refugia during Pleistocene cold phases. Nuclear markers indicate varying degrees of admixture between these southern refugial populations upon secondary contact. The occurrence of divergent mitochondrial lineages elsewhere in the range of B. arietans indicates the possibility of cryptic speciation. This hypothesis is tested using recently developed coalescent
species delimitation approaches applied to data from anonymous nuclear markers. This supports the existence of six candidate species, although corroborative evidence and/or increased geographic sampling will be required before taxonomic changes are justified.
Overall, this thesis provides a significant advance in our understanding of the
evolutionary history of Bitis. The results also highlight several priorities for future research on these snakes.