Phylogenetic Relationships, Biogeography and Species Delimitation: A case study on southern African Silene (Caryophyllaceae)

Abstract

The primary aim of this thesis was to explore the phylogenetic relationships and historical biogeography of African members of the plant genus Silene (Caryophyllaceae), with special focus on the eight native southern African taxa. Three loci (the nuclear ribosomal internal transcribed spacer region, and the rps16 and matK regions from the plastid genome) generated using traditional Sanger sequencing were used to infer the phylogenetic positions of African taxa, while sequence data from 28 low copy nuclear loci were generated using the target capture method to explore shallow phylogenetic relationships within southern African taxa. Bayesian multispecies coalescent methods (StarBeast2, STACEY) were used for species-tree estimation with historical diffusion models (GEO_SPHERE) used simultaneously to infer the biogeographic origins of the monophyletic groups identified. The results indicate that southern African members of Silene belong to two different groups (sect. Elisanthe and Silene) which are relatively distantly related and have different colonisation histories in southern Africa. For North African species of Silene, similar analytical approaches resolved the phylogenetic positions of many hitherto understudied taxa but with lack of resolution in the deeper nodes. By leveraging the large amount of sequence data produced via target capture from a comprehensive sample of southern African section Elisanthe the monophyly and phylogenetic relationships of S. rigens, S. saldanhensis, and S. ornata, all local endemics to the South African southwest coast, were resolved and in agreement with a recently established taxonomy. However, the results also indicate that the widespread S. undulata may not be monophyletic. Several recovered well supported clades within S. undulata are congruent with geographical distribution rather than ecology, indicating a spatial differentiation pattern. The work carried out in this thesis demonstrates that target capture sequencing is a valuable method for generating informative sequence data and useful for resolving phylogenetic relationships at shallow levels. Additionally, the thesis also demonstrates how phylogenetic analyses performed under explicitly parameterized statistical models such as the multispecies coalescent can be expanded by incorporation of other sources of information (e.g., biogeographic) to better understand evolutionary relationships of young lineages and thus inform or test existing taxonomic classifications.