Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Knowledge of the diversity and evolutionary histories of insects in South Africa’s fynbos biome lags far behind what is known of the plant groups that make up this global biodiversity hotspot. To address this imbalance, I undertook a molecular phylogenetic study of fynbos-endemic Cephalelini leafhoppers that specialise on restios in the family Restionaceae. My phylogenetic results did not recover the South African Cephalelini as monophyletic, nor did I find monophyly of described species, but several monophyletic clades of species were found within Cephalelini. Furthermore, phylogenetic dating suggested that the divergence between South African and Australian Cephalelini post-dates Gondwanan vicariance, implying intercontinental extreme long distance dispersal of these insects ca. 5-11 MYA. Diversification within the Cephalelini is also much more recent than that of the Restionaceae hosts on which they specialise, negating the possibility of coevolution between plants and insects. Rather, analysis of phylogenetic conservatism of host use reveals that Cephalelini evolution has tracked the evolution of their Restionaceae hosts and that closely related insects feed on the same plant host tribes. A finer scale of tracking of host evolution (such as at the clade or genus level) is expected when taking into account how highly specific I find Cephalelini host use to be, but its absence might be explained by the recent divergence of Cephalelini relative to the age of Restionaceae. Analysis of conservatism of host use was also carried out using a phylogeny of the Restionaceae, and revealed that, overall, Cephalelini host use and avoidance have no phylogenetic bias, indicating many empty potential niches for Cephalelini, or alternately that host use is governed by factors which are phylogenetically unconstrained. Lastly, I also analysed the evolution of specialisation of Cephalelini and find no trend towards increased specialisation within the group, which is contrary to what is expected of the evolution of herbivorous insects. Overall, this study presents the first evidence of intercontinental dispersal of insect fauna between South Africa and Australia and as such highlights an unconsidered factor in the accumulation of faunal diversity in the fynbos biome. I find Cephalelini to be highly specialised in their host preference, but this pattern only becomes apparent at the tribal host level in the evolution of Cephalelini. Although Cephalelini are highly specialised, I find no evidence of evolution towards increasing specialisation within the group. / AFRIKAANSE OPSOMMING: Ons kennis van die evolusie van fynbosinsekte is redelik beperk vergeleke met hoe veel ons weet van die plante wat die merkwaardige diversiteit van die fynbos-bioom uitmaak. In `n poging om hierdie wanbalans reg te stel het ek `n molekulêr-evolusionêre studie onderneem van die fynbos-endemiese blaarspringer-groep Cephalelini, wat op Restionaceae-gasheerplante spesialiseer. Ons het drie geen-areas geamplifiseer vir filogeniekonstruksie en dateringsdoeleindes: insek-kern H3, insek- mitokondriaal COI en insek-simbiont Sulcia 16S. Met behulp van filogenetiese analise is bevind dat die Suid-Afrikaanse Cephalelini nie `n monofiletiese groep is nie en dat beskryfde spesies ook nie monofileties is nie, maar verskeie monofiletiese spesie-groepe is wel gevind. `n Oorkruis-gevalideerde dateringsoefening dui aan dat divergensie tussen Suid-Afrikaanse en Australiaanse Cephalelini meer onlangs as die verbrokkeling van Gondwana plaasgevind het, wat impliseer dat daar uitruiling van insekte tussen die kontinente oor die afgelope 5-11 MJ plaasgevind het. Die diversiteit van Cephalelini het ook veel meer onlangs ontstaan as dié van hulle Restionacaea-gashere wat beteken dat ko-evolusie in die eng sin nie moontlik is nie. ‘n Ontleding van die evolusie van gasheer-keuse deur Cephalelini dui wel aan dat Cephalelini-evolusie die patron van hul Restionaceae-gashere volg en dat naverwante Cephalelini dieselfde stam van Restionaceae as gashere verkies. Die bevinding dat die Cephalelini hoogs gespesialiseerd is in hulle gasheer-keuses lei ‘n mens tot die verwagting dat die evolusie van Cephalelini meer getrou die evolusie van hulle gashere sal volg as wat wel die geval is (dalk op die vlak van groep of genus), maar die relatiewe jeugdigheid van die Cephalelini vergeleke met die ouderdom van die Restionaceae is moontlik die rede hiervoor. Analise van gasheer-keuse is ook uitgevoer op `n filogenie van die Restionaceae wat aantoon dat daar nie ‘n beperking van verwantskappe is tussen gashere wat verkies of verwerp word nie, wat daarop dui dat daar `n menigte nisse is wat oënskynlik onbenut is, of dat Cephalelini gasheer-keuse bepaal word deur `n Restionaceae-eienskappe wat nie filogeneties beperk is nie. Laastens het ek die evolusie van spesialisering deur Cephalelini ontleed, maar geen neiging tot toenemende spesialisering binne die groep gevind nie, wat onverwags is in die lig van vorige studies. As `n geheel bied hierdie studie die eerste bewys van die uitruiling van insek-fauna tussen die Suid-Afrikaanse fynbos-bioom en ander kontinente, wat `n onopgetekende invloed op die diversiteit van diere in die fynbos is. Cephalelini is `n hoogs gespesialiseerde groep insekte, maar uit `n filogenetiese perspektief word dit eers waargeneem op die vlak van gasheerstam. Ten spyte van hulle hoë vlak van spesialisering het ek geen bewys gevind van `n toename daarin binne die evolusie van die groep nie.

Two separate phylogenetic studies were performed for two different taxonomic levels within Hymenoptera. The first study examined the utility of expressed sequence tags for resolving relationships among hymenopteran superfamilies. Transcripts were assembled from 14,000 sequenced clones for 6 disparate Hymenopteran taxa, averaging over 660 unique contigs per species. Orthology and gene determination were performed using modifications to a previously developed computerized pipeline and compared against annotated insect genomes. Sequences from additional taxa were added from public databases with a final dataset of 24 genes for 16 taxa. The concatenated dataset recovered a robust and well-supported topology; however, there was extreme incongruity among individual gene trees. Analyses of sequences indicated strong compositional and transition biases, particularly in the third codon positions. The use of filtered supernetworks aided visualization of the existing congruent phylogenetic signal that existed across the individual gene trees. Additionally, treeness triangle plots indicated a strong residual signal in several gene trees and across codon positions in the concatenated dataset. However, most analyses of the concatenated dataset recovered expected relationships, known from other independent analyses. Thus, ESTs provide a powerful source of information for phylogenetic analysis, but results are sensitive to low taxonomic sampling and missing data. The second study examined subfamilial relationships within the parasitoid family Braconidae, using over 4kb of sequence data for 139 taxa. Bayesian inference of the concatenated dataset recovered a robust phylogeny, particularly for early divergences within the family. There was strong evidence supporting two independent lineages within the family: one leading to the noncyclostomes and one leading to the cyclostomes. Ancestral state reconstructions were performed to test the theory of ectoparasitism as the ancestral condition for all taxa within the family. Results indicated an endoparasitic ancestor for the family and for the non-cyclostome lineage, with an early transition to ectoparasitism for the cyclostome lineage. However, reconstructions of some nodes were sensitive to outgroup coding and will also be impacted with increased biological knowledge.

Abies is the second largest genus of family Pinaceae (after Pinus), consisting of about 51 species, all native to the Northern Hemisphere. There are six native taxa belonging to this genus growing in pure and mixed stands in Turkey. Abies cilicica subsp. isaurica, Abies nordmanniana subsp. bornm&uuml / lleriana, Abies nordmanniana subsp. equi-trojani, Abies x olcayana are endemic and considered as lower risk (LR) species. To determine the genetic relationships in Turkish firs, 18 populations of different subspecies of Abies were collected from different regions of Turkey and non-coding trn regions of chloroplast DNA were sequenced to assess the genetic structure of the studied species. trnL, trnF and trnV region were examined. All the trn regions of Abies species in the world (aproximately 300 species that found in the IPNI (The International Plant Names Index) were investigated in the database of NCBI. The available trn sequences of 23 Abies species worldwide included into the analyses. All analyses to estimate molecular diversity parameters were carried out with the MEGA software. The constructed phylogenetic tree with the trn sequences revealed that Turkish firs formed a monophyletic group with almost no sequence divergence. v Since sequence data for all three sectors of trn were not available from the NCBI data base, the phylogentic analysis with the sequence data of trnL regions were compartively analyzed in all firs. The results showed that Turkish- European species formed a single clade, which clearly differentiated them from the others, such as Japanese species, A. veitchii. Similarly, according to the sequence data of trnF, Turkish fir species were grouped together and distinctly separated from Asian-American Fir species. The results suggest that all Turkish firs may have evolved from single ancestral fir species, most likely from Abies nordmanniana.