Department of Botany and Zoology

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An assessment of the subgeneric classification of Zygophyllum (Zygophyllaceae) in Southern Africa : evidence from noncoding trnL-trnF chloroplast DNA sequences
(Stellenbosch : Stellenbosch University, 2001-04) Makwarela, Azwimpheleli M.; Bellstedt, D. U.; Dreyer, L. L.; Marais, E. M.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Sequence data from the intron and the spacer of the trnL-F chloroplast DNA region were used to study the phylogenetic relationships of the genus Zygophyllum L. (Zygophylloideae: Zygophyllaceae) in the southern African region. The chloroplast DNA was extracted from both herbarium and silica-gel dried material. Closely related genera, i.e. Augea Thunb., Fagonia L. and Tetraena Maxim. within the subfamily Zygophylloideae and more distantly related genera Seetzenia R.Br. ex Decne and Tribulus L. were used as outgroups. Sequences revealed length variation mainly due to the presence of indels (insertions and deletions). Phylogenetic analysis using parsimony revealed two distinct lineages for southern African members of Zygophyllum, corresponding to the proposed subgeneric classification (Van Huysteen 1937; Van Zyl 2000). There is a strong monophyly support for the sections within the subgenus Agrophyllum (Neck.) Endl. However, the transference of the monotypic section Grandifolia Engl. from subgenus Zygophyllum to Agrophyllum is not confirmed, because material of Z. stapffii Schinz. was not available. Despite the morphological evidence for the subdivision of the subgenus Zygophyllum, the molecular data did not confirm the monophyly for its sections. This could be the result of biased sampling, since all the species used in the analyses, except Z. cordifolium L.f. and Z. morgsana L., belong to section Capensia Engl. The trnL region data support the transfer of the mono typic section Morgsana Huysst. from subgenus Agrophyllum to subgenus Zygophyllum. The molecular data also seem to have implications for the biogeography of Zygophyllum. The southern African Agrophyllum representatives are related to East African and Middle East Zygophyllum species, whereas the southern African subgenus Zygophyllum members are closely related to Australian Zygophyllum species.
A biosytematic [i.e. biosystematic] study of the seven minor genera of the Hyacinthaceae
(Stellenbosch : Stellenbosch University, 2002-03) Van der Merwe, Alison M. (Alison Mary); Marais, E. M.; Bellstedt, D. U.; Stellenbosch University. Faculty of Sciences. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: A biosytematic revision of the seven minor genera of the Hyacinthaceae, including twenty-two species, was undertaken. Muller-Doblies & Muller-Doblies (1997) considered these seven genera (Amphisiphon Barker, Androsiphon Schltr., Daubenya Lindl., Massonia Thunb. ex Houtt., Neobakeria SChItL, Polyxena Kunth and Whiteheadia Harv.) together with the genus Eucomis L'Herit. to form the subtribe Massoniinae of the tribe Massonieae. Previous revisions of the group were based only on morphological characters (Jessop 1976; Muller-Doblies & Muller-Doblies 1997). The subtribe Massoniinae is characterised by the large variety of floral forms exhibited by the different species in the group. In the past this has led to the establishment of many monotypic genera for species thought to have unique floral structures. Morphological, leaf anatomical, palynological, geographical and molecular data were studied in order to delimit the taxa and determine the phylogenetic relationships within the group. This showed that most of the unique floral structures are probably only adaptations to pollination strategies and all except one of the monotypic genera are now placed in the genus Daubenya. In the genus Massonia there is a great deal of variation in leaf morphology and this resulted in the establishment of many invalid species, now mostly reduced to synonymy. A new species was described, several name changes made and several species were reduced to synonymy.
Molecular ecology of two invasive legumes (Acacia saligna and Paraserianthes lophantha)
(Stellenbosch : Stellenbosch University, 2012-12) Thompson, Genevieve Dawn; Richardson, David M.; Le Roux, Johannes J.; Wilson, John R.; Bellstedt, D. U.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Large-scale human-mediated movements of organisms promote the establishment of species outside their native ranges and a very small proportion of these species become invasive. Invasive species management typically assumes that introduced species are single, static evolutionary units that are genetically analogous to their native counterparts. However, studies have shown that native and introduced populations of a number of introduced plants differ vastly in their genetic composition. These differences may negatively affect the overall success of control and management programmes, particularly for species that are intra-specifically diverse. The influence of intra-specific diversity on the invasion process was tested in two widely exported tree species that are native to Western Australia, Acacia saligna (three subspecies) and Paraserianthes lophantha (two subspecies). Climate matching between the native and introduced range (using species distribution models, SDM) is widely used to forecast future invasion risks, however, it is unknown if SDMs can detect intra-specific niche differences in invasive plants. The SDMs I developed for the subspecies of A. saligna detected intra-specific differences within the native range, but did not predict the full invasive distribution in South Africa. Unsurprisingly, SDMs agreed with genetic analyses (based on nuclear microsatellites, nuclear DNA, and chloroplast DNA) and did not assign South African populations to any subspecies of A. saligna. South African populations were assigned to a novel genetic entity likely produced by human cultivation practices. A global phylogeny identified this cultivated genotype in introduced populations in eastern Australia and Portugal, while the remaining introduced populations differed markedly in their genetic composition. Overall, A. saligna‘s high intra-specific diversity and complex introduction history generated a variety of genetic patterns across the current global distribution of the taxon. Global populations of P. lophantha were processed using a similar approach to that used for A. saligna, and aimed to determine if the same pathways and modes of introduction produced analogous genetic patterns in a closely related species. Diverse arrays of genotypes were identified in introduced populations of P. lophantha, suggesting inconsistent sampling of a variety of native sources. Further work is however needed to clarify the morphological and genetic differences (if any) between the intra-specific entities, and identify exactly which P. lophantha subspecies were introduced outside of their native range, The variation in the global distribution of genetic diversity observed in A. saligna and P.lophantha demonstrated that intra-specific genetic variation, human usage, and the pathway and manner of introduction interact during several phases of the invasion process and collectively determine the introduced genetic patterns. The dissimilarity in the distribution of genotypes in both species suggests that they might not behave the same way throughout their introduced range. Consequently, management insights might not be transferrable between regions. More generally, my findings provide an important contribution to the debate whether (and how quickly) introduced and native populations should be treated as fundamentally different entities.
A molecular phylogenetic assessment of Oxalis L. section Angustatae subsection Lineares using trnL-trnF sequence data
(Stellenbosch : Stellenbosch University, 2003-03) Oberlander, Kenneth; Dreyer, L. L.; Bellstedt, D. U.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: The phylogenetic relationships and taxonomic status of South African Oxalis L. species are highly unresolved, both regionally and with regard to precise placement within the genus as a whole. Studies based exclusively on morphological and palynological characteristics have hitherto proved only partially successful in resolving natural groupings among the indigenous taxa of the region. Recent studies involving a few native taxa have indicated the plastid trnL-trnF non-coding DNA region as useful for the purposes of reconstructing phylogenetic relationships within the genus. The present study addressed the taxonomic monophyly and relationships of the highly unresolved section Angustatae subsection Lineares, using DNA sequence data. The phylogenetic reconstruction of southern African Oxalis species renders five of the subsections of section Angustatae sensu Salter (1944) polyphyletic, three of them conclusively so. The members of subsection Lineares are split between three clades, two of them with strong bootstrap support. None of these three clades consists exclusively of species of subsection Lineares. Likewise four of the seven assemblages of related taxa within subsection Lineares sensu Salter (1944) are not retrieved as monophyletic. Pollen data sensu Dreyer (1996) supports the clades retrieved in this study, whereas very few morphological characters could be plotted as potential synapomorphies for these clades. The resultant phylogenetic reconstruction thus supports palynological data of this subsection, and indicates the urgent need for a revision of the current morphological classification of Salter (1944).
Molecular phylogeny, radiation patterns and evolution of life-history traits in Ursinia (Anthemideae, Asteraceae)
(Stellenbosch : Stellenbosch University, 2008-12) Swelankomo, Nonkululeko; Mucina, Ladislav; Bellstedt, D. U.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
Sequence data from the Internal Transcribed Spacer (ITS) of the nuclear ribosomal DNA were used to study the phylogenetic relationships in the genus Ursinia Gaertn. (Asteraceae, Anthemideae) in the southern African region. Closely related genera, i.e. Cotula L., Osteospermum L. and Agoseris Raf., were used as outgroups. The study also included maximum parsimony and principal component analyses. The taxa within the genus Ursinia had previously been classified into two subgenera, Ursinia and Sphenogyne R.Br., mainly on the basis of distinct cypsela characters. The maximum parsimony, principal component and the phylogenetic analyses revealed two subgenera, corresponding to the existing subgeneric classification. Principal component analysis shows that the pappus, the number of pappus bristles and the colour of the cypsela are the most informative characters. However, the low number of phylogenetically informative characters of the ITS sequences, the poor resolution in the consensus tree, and low branch support values indicate that the ITS data contain weak phylogenetic signals. The low bootstrap values for many nodes suggest that one should be cautious in using the ITS region alone to make final conclusions about the origin and evolution of taxa. In maximum parsimony analysis, the RI, CI and bootstrap values are low; principal component analysis values are also low. Furthermore, there is a lack of resolution in subgenus Sphenogyne. In the literature, Ursinia is divided into seven series but they were not retrieved as monophyletic in this study, probably because of short branch lengths in the phylogeny. Further molecular data are therefore required to be able to support or reject the present classification. Maximum parsimony, principal component and molecular analyses show that U. trifida f. calva Prassler and U. trifida (Thunb.) N.E.Br. f. trifida are not sister taxa, supporting the recognition of these two taxa as separate species. The Ursinia taxa from the summer-rainfall region are not monophyletic and are sister to a clade of Cape species. This supports a hypothesis that Ursinia migrated from the Cape into the Drakensberg which has been shown for a number of other Cape groups that have Drakensberg relatives.
Molecular systematic study of Southern African Oxalis (Oxalidaceae)
(Stellenbosch : University of Stellenbosch, 2009-03) Oberlander, Kenneth Carl; Dreyer, L. L.; Bellstedt, D. U.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.
The genus Oxalis forms a major part of the flora of southern Africa, in particular the Cape Floristic Region (CFR) at the southwestern tip of the continent, but the current taxonomy is outdated and ecological knowledge of the lineage is sadly incomplete. In this thesis I set out to address several aspects of Oxalis systematics that urgently require attention. Firstly, the current macro-morphological taxonomy requires phylogenetic testing, as it is acknowledged to be incomplete and artificial. I address this need by providing a DNA sequence-based phylogeny of three markers, using three different inference methods, for nearly three quarters of the indigenous species. This phylogeny confirmed both the monophyly of the southern African taxa, and the artificiality of the current classification system. It is congruent with previous sequence-based reconstructions of smaller groups of southern African Oxalis species, and with the palynological classification proposed for the genus. Secondly, previous phylogenetic work on the southern African members could not resolve basal relationships within the southern African clade. I attempt to address this problem by sequencing three extra chloroplast markers for a select group of taxa, followed by separate and combined (total evidence) molecular phylogenetic analyses. This approach did increase resolution at the base of the southern African lineage, but many clades still showed poor resolution and support despite the use of more than 7 000 bases of sequence data. Resolving these clades within the southern African Oxalis phylogeny remains a challenge, and should prove a fertile field for future research. Thirdly, the ages (and thus duration of presence) of many Cape plant lineages within the CFR are of major interest, given that the CFR represents a global biodiversity hotspot. The age of the genus in the Cape is estimated by analyzing combined sequence data for all sampled taxa under both a Bayesian Relaxed Clock and a semiparametric Penalised Likelihood method, using calibration points inferred from Relaxed Clock analyses of the entire order Oxalidales, for which fossil data are available. In an attempt to account for known problems with divergence time estimation, I explored the potential bias introduced by method used, marker genome source and different calibrations on the root. The results indicate substantial variation in the age of crown southern African Oxalis over a nearly twenty million year period, varying according to source data, calibration estimate and methodology employed in the reconstruction. Despite this major variability, all average estimates are older than iv 18 million years, which agrees with a growing body of evidence that there has been a gradual accumulation of floristic diversity in the CFR, rather than a rapid, recent burst of speciation. Fourthly, as the produced phylogenies conclusively show the artificial nature of the current taxonomy, I propose a new, almost completely different classification for southern African Oxalis taxa. Although a significant improvement, this classification is considered informal due to the complete disagreement between the old and proposed new taxonomies, poor resolution in some of the proposed lineages, and a need to confirm proposed groups (clades) with the identification of morphological synapomorphies. Potential synapomorphies for various clades are proposed and discussed, which should guide future research. Fifthly, the presence of bulbs in this genus is of great interest as a potential preadaptation for seasonally arid climates. The evolution of the bulbous habit in Oxalis is here explored for the first time. I address the sequence of major morphological character state changes leading to the suite of characters corresponding to the bulbous habit. The homology of basal leaf petioles, fleshy leaf scales and tunics is discussed, and it is shown that many bulb characters present in the southern African lineage are also found in the close relatives of this lineage, and are thus older than this lineage. The ecological and evolutionary implications of bulb geophytism in the CFR Oxalis are also discussed. Finally, I address certain taxonomic issues that arose during the course of this study. Co-authors and I describe the new species O. saltusbelli and O. ericifolia. We also clarify issues surrounding the tremendously variable group species O. flava and propose some nomenclatural changes and synonyms for related taxa. We also address the taxonomic position of the rare species O. purpurata, which was located too late in the course of this study to include in the main analyses.
Phylogenetic and population genetic studies in the genus Streptocarpus Lindl. (Gesneriaceae DC.)
(Stellenbosch : Stellenbosch University, 2008-12) De Villiers, Margaret Jenifer; Bellstedt, D. U.; Moller, M.; Dreyer, L. L.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
Streptocarpus Lindl. (Gesneriaceae DC.) is a genus of herbaceous plants containing approximately 160 species, of which the majority occur in Africa and Madagascar. They are largely restricted to shaded and moist habitats such as primary forest and rock outcrops. The genus contains considerable morphological variation, with subgenus Streptocarpella containing caulescent species and subgenus Streptocarpus mostly consisting of acaulescent growth forms, mainly the unifoliates, plurifoliates and rosulates. Preliminary molecular analyses conducted using nuclear ITS sequence data suggested that subgenus Streptocarpus evolved in tropical central Africa, before radiating in several independent waves into southern Africa. Streptocarpus has therefore only recently spread into South Africa. Amongst the South African species, 11 morphologically similar species were identified as being closely related, together forming the Cape primrose clade, based on the analysis of nuclear ITS sequence data. However, these analyses only contained a few South African species, and the ITS data did not provide enough resolution of relationships within this clade. In this study nuclear and chloroplast sequence data as well as nuclear microsatellite data were therefore employed to unravel the complex relationships amongst the South African Streptocarpus species. The analyses indicate that 16 rosulate, palynologically similar species (S. primulifolius, S. rexii, S. johannis, S. baudertii, S. modestus, S. formosus, S. gardenii, S. lilliputana, the S. cyaneus complex [S. cyaneus, S. parviflorus, S. fenestra-dei, S. kunhardtii and S. roseo-albus], S. floribundus, S. aylae and S. kentaniensis), the core Cape primrose species, are closely related, while five unifoliate/plurifoliate, palynologically more variable species (S. denticulatus, S. dunnii, S. pusillus, S. rimicola and S. bolusii) consistently emerged as more distantly related to the core Cape primrose species. However, the positions of a further ten species (S. meyeri, S. montigena, S. fanniniae, S. caeruleus, S. longiflorus, S. polyanthus, S. saundersii, S. porphyrostachys, S. grandis and S. vandeleurii) were more complex in the analyses, indicating that hybridization has played a role in their evolution. Five of these species (S. meyeri, S. montigena, S. fanniniae, S. caeruleus and S. longiflorus) are, however, palynologically homogenous and rosulates, and therefore are probably more closely related to the core Cape primrose species, while the other five (S. polyanthus, S. saundersii, S. porphyrostachys, S. grandis and S. vandeleurii) are unifoliates/plurifoliates that are palynologically more heterogenous, and are probably more distantly related to the core Cape primrose species. Amongst the core Cape primrose species, S. primulifolius emerged as being ancestral or having hybridized with many of the other species, while the S. cyaneus complex forms a geographically and genetically more isolated group. However, evolutionary relationships amongst these species were to a certain extent obscured by incomplete lineage sorting caused by limited interpopulation gene flow, frequent hybridization and rapid speciation. The analyses confirmed that the Pondoland Centre forests constitute important Pleistocene refugia, and revealed some of the historical migration routes along which the species had radiated.
Preliminary investigations into the phylogenetic relationships in the genus Erica L.
(Stellenbosch : University of Stellenbosch, 2006-12) Lester, Ntsikelelo Blessings; Bellstedt, D. U.; Dreyer, L. L.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Erica is a genus of about 860 species world wide, with 700 of these found in South Africa’s southwestern and southern Cape, making it by far the most speciose genus in the Cape Floristic Region. This poses a particular challenge in the construction of a molecular phylogeny of the genus. The choice of suitably variable gene regions is a crucial decision on which the successful phylogenetic reconstruction of this important genus is critically dependent. The aim of this project was therefore to determine which DNA regions, both chloroplast and nuclear, would be sufficiently variable to give adequate informative characters that may be useful at the species level phylogenetic reconstruction. A subset of 30 species, representing the range of morphological diversity and pollinator preference within Erica, was selected for study. For each of these species the variability in eight chloroplast regions (trnL-F, matK, trnS-G, rps12- rpl20, psbAtrnH, trnC-D, rps4-trnT and trnT-L) and the nuclear ITS region was investigated. The psbA-trnH, trnC-D, rps4-trnT and trnT-L chloroplast regions were found to be problematic to amplify and to possess too few Parsimony Informative Characters to be of use in phylogenetic reconstruction. Four of the chloroplast regions, trnS-G, trnL-F, matK and rpS12-rpL20 and the nuclear ITS region could be amplified and sequenced with success. The ITS region was found to be reasonably variable, with the chloroplast genes showing less variability. The DNA extraction method employed showed itself to be of critical importance in the success of the study. Two DNA extraction protocols, both modified from the original Doyle and Doyle (1987) method, were tested. The one included double the amount of β-mercaptoethanol and Polyvinylpyrrolidone (PVP) and the other included an extended phenol: chloroform: isoamylalcohol step. These variables, together with the effectiveness of these methods on fresh vs. silica dried plant samples, were investigated to determine which of the two would yield high quantities and qualities of DNA and result in the best method for the extraction of DNA from Erica species.

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