Browsing by Author "Verboom, Tony"
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- ItemRestrictedComparative metabolomic profiling of phenolics in the desiccation-tolerant “resurrection plant” Myrothamnus flabellifolia (Myrothamnaceae) using conventional and green chemistry-based solvent systems(2019) Bentley, Joanne; Verboom, TonyMyrothamnus flabellifolia (Myrothamnaceae) belongs to a group of ±300 angiosperm species known as “resurrection plants” that exhibit vegetative desiccation tolerance. They are able to survive dehydration to an air-dry state, tolerating up to 95% cellular water loss for a prolonged period of time followed by the rapid recovery of metabolism in the tissues within 24–72 h of rehydration. Prolonged cellular water loss is deleterious and is associated with the production of reactive oxygen species (ROS), which causes cellular degeneration, and ultimately, death. Resurrection plants have evolved various strategies to ameliorate this damage, including biochemical, ultrastructural, and anatomical modifications. Myrothamnus flabellifolia is widespread across southern Africa, and within its range it occurs in regions that experience high, moderate, and low rainfall; the low rainfall region also being associated with longer dry periods. Myrothamnus flabellifolia has historically been used for the treatment of chest infections, uterine pain, and gingivitis, and, more recently, has been shown to exhibit various phytochemical activities relating to the potential inhibition of diabetes, reverse transcriptases, and microbes. Previous studies have found M. flabellifolia extracts to contain high levels of polyphenolic compounds, which act as protectants against the ROS-induced damages caused by prolonged periods without moisture. However, a global assessment of the phenolic constituents, including anthocyanins, present in M. flabellifolia from across its geographic range is currently lacking. As the biosynthesis of compounds is likely to be subject to a fair amount of environmental control, an evaluation of the molecules present in this species from across its geographic range is warranted. Thus, in this study, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics approach was used to screen for phenolic compounds, including anthocyanins, from leaf material sampled in the field from eight populations representing the western, southern, and eastern range of the species distribution. Putative phenolic compounds were identified based on their MSE spectra in the negative ionisation and positive ionisation (for anthocyanins) modes. Their potential roles in the ROS-scavenging capacity of this plant were also discussed. Using this information, multivariate statistics were used to compare the phenolic profiles of the different populations in order to ascertain whether plants from the different regions were associated with any particular phenolic signature, and this was also evaluated against a phylogenetic hypothesis for species relationships based on three non-coding chloroplastic markers. Additionally, a preliminary green chemistry-based extraction protocol using Natural Deep Eutectic Solvents was also used to further screen for phenolic compounds, and this was compared against the conventional organic solvent system. Several phenolic compounds not previously detected in M. flabellifolia were putatively identified, many of which, based on an assessment of the literature, are associated with high antioxidant activity. The phylogenetic analyses suggested that the Namibian plants are more highly diverged than the South African and Malawian plants. The metabolomics analysis corroborated the DNA analysis, in that the most differentially expressed ions in the Namibian population were able to discriminate these samples from both the Malawian and South African samples. While the phenolic profiles of the samples collected from the same countries were similar, there was reasonable withinpopulation variability in those collected from South Africa and Malawi. Conversely, the Namibian samples exhibited far less variability, suggesting that a particular suite of protective compounds may be required for survival in that comparatively drier region. A Natural Deep Eutectic Solvent-based system successfully targeted phenolics in M. flabellifolia and thus constitutes a potential future green chemistry solution for phytochemical investigations in medicinal plants.
- ItemOpen AccessThe evolution and prevalence of reproductive assurance in the genus Lachenalia(2013) Rink, Ariella; Verboom, Tony; Rodger, JamesSince its proposal by Darwin (1876), the concept of reproductive assurance (RA) has been much discussed, modified and tested. It is hypothesized to occur under pollen- and/or mate-limitation, each of which can arise in a multitude of manners, and RA itself takes many forms. Here its evolution and prevalence in the genus Lachenalia (Asparagaceae) is investigated. The genus exhibits many of the characteristics suggested in the literature to be associated with reproductive assurance, including intraspecific polyploids, vegetative reproduction and self-compatibility. Of the 27 study species, 20 were found to be self-compatible and four were capable of autonomous self-pollination. Pollinator-dependent species were found to have more attractive floral display structures. The five species exhibiting intraspecific polyploidy were all self-compatible. Offset production, known to occur in many Lachenalia species, was thought to exhibit a negative association with self-compatibility. No significant association, however, was found. A deeper understanding of the patterns of reproductive assurance in the genus requires study of the mechanisms enforcing self-incompatibility, and of the ecological and physiological correlates of reproductive assurance, is needed.
- ItemOpen AccessExploration of climate mediated decline in a critically endangered southern hemisphere conifer over the last 40 years / Annabelle J. Rogers(2013) Rogers, Annabelle J; February, Edmund C; Verboom, TonyWiddringtonia cedarbergensis is a critically endangered conifer restricted entirely to the Cederberg Mountain range in the Western Cape of South Africa. This study aimed to assess whether contemporary climate change could be a driver in the recently documented tenfold decline of W. cedarbergensis in the last 40 years. By building distribution models using Maxent bioclimatic modelling for pre- and post- 1970’s point occurrence data, the distribution of the species pre- and post-1970’s were compared and assessed for significant change. Models predicted a clear range contraction in W. cedarbergensis from pre- to post- 1970. The present model predictions of suitability occur in a tight altitudinal band on the mid to upper slopes of the middle Cederberg (minimum of 1048m to a maximum of 1530m). However, the climatic predictions associate the present model distribution with relatively warmer and drier areas compared to that of the pre- 1970 model, suggesting a shift down slope rather than upslope. This is possibly due to the exaggeration of the upper limit of distribution for the pre-1970’s model that predicts W. cedarbergensis to occur as high as 1850m. This is unlikely due to the high prevalence of frost at this elevation. Though any climatic signal was complicated due to historical data error, high confidence in the present model prediction adds a valuable contribution to a body of literature that documents the decline of W. cedarbergensis and has important implications for conservation management of the species.
- ItemOpen AccessMechanisms determining the coexistence of open- and closed-canopy biomes(2018) Power, Simon C; Cramer, Michael; Bond, William; Verboom, TonyOpen- (e.g. grassland, savanna, shrubland) and closed-canopy (e.g. forest) biomes frequently coexist in the same landscape, where open environments tend to be fire-prone with higher light, but lower nutrient and water availability than closed environments. Environmental heterogeneity could select for divergent floristic assemblages and adaptive traits, from which emergent differences in resource availability and fire incidence contribute to excluding species from the alternate habitat. In this thesis, I investigated whether the coexistence of open–closed canopy biomes, such as forest and fynbos in the Cape Floristic Region, is contingent on environmental heterogeneity coupled with contrasting species traits. Given the heterogeneity in multiple environmental properties between open- and closed-canopy biomes, I hypothesized that boundaries between open- and closed-canopy biomes will display greater floristic turnover compared to boundaries between structurally similar biomes (e.g. open- and opencanopy biomes). To explore this, genus- and family-level turnover were correlated with climate, fire, leaf area index (LAI: proxy for understorey light) and soil properties across biome boundaries in South Africa. Both genus- and family-level turnovers were highest across open–closed boundaries and most strongly predicted by increased differences in LAI, suggesting that contrasting light regimes provide significant adaptive challenges for plants. The potential effect of contrasting light regimes is highlighted by the absence of open-canopy species from forest understoreys, where low, dynamic light could limit the ability of plants to acquire sufficient carbon. This apparent shade intolerance led to the hypothesis that open-canopy species lack the traits to maintain a positive carbon balance under low and dynamic light. To test this, leaf traits and photosynthetic response to continuous or dynamic light were compared between forest and fynbos species grown under three light treatments. Fynbos species experienced high mortality under shade treatments, produced leaves that were thicker, up to 1000 times smaller, had lower photosynthetic rates (0.8 versus 3.4mol m-2 s -1 ) under continuous low light (400 mol m-2 s -1 ) and lower light-use efficiency during dynamic light sequences than forest species. These differences imply that shade intolerance in fynbos species is associated with traits that are inefficient at harvesting light and require relatively continuous high intensity light for carbon assimilation. Moreover, these inefficiencies would make it difficult to support the carbon intensive traits (e.g. cluster roots, lignotubers, sclerophyllous leaves) that facilitate fire survival and nutrient acquisition/conservation in open habitats. In contrast, forest species are able to colonize open habitats during the long-term absence of fire, implying that they are able to tolerate high light and low nutrient conditions. Given that plants frequently cope with contrasting conditions through the expression of phenotypic plasticity, it was hypothesized that closed-canopy species possess greater plasticity than open-canopy species. To assess this, the response of leaf traits and foliar nutrition to changes in LAI and soil nutrition were compared between forest and fynbos species in the field. Leaf size and specific leaf area in forest species correlated positively with LAI and soil nutrition, whereas fynbos species response was weak, suggesting that forest species are more plastic. This plasticity may be realised by the variable light conditions forest species experience through their canopy and the occupation of higher nutrient soils, which alleviate belowground constraints. By comparison, the occupation of low nutrient soils by fynbos may inhibit plasticity given the selection of inflexible, conservative leaves. Consequently, I propose that the coexistence of open- and closed-canopy biomes arises from the steep turnover in selective regimes, which together with the contrasting adaptive traits and degrees of phenotypic plasticity they require, act together to competitively exclude species from the alternate habitat.
- ItemOpen AccessMollecular Phylogeny of tribolium (Danthoniodeae: Poaceae) and its taxonomic implications(2003) Ntsohi, Refiloe; Verboom, TonyMolecular sequence data from two noncoding regions of D A (ITS AND TRNL-F) Were used to produce a phylogeny for the genus Tribolium and its African and Australasian allies. Topological comparisons of the combined molecular data with the appended existing morphological tree were made. A significant incongruence was revealed. Molecular data indicate that Tribolium is paraphyletic. The formally defined sections: Uniolae, Acutiflorae and Tribolium have been retrieved by the molecular data. The analysis retrieved Karroochloa as polyphyletic. Monophyly of Schismus is strongly supported. The Australasian species form a monophyletic clade. Data support early divergence of the Merxmuellera species and Pseudopentameris macrantha.
- ItemOpen AccessPhylogenetic studies in the genus Jamesbrittenia tribe Manuleae, family Scrophulariaceae(2006) Herron, Margaret; Verboom, TonyJamesbrittenia is a genus of 84 largely perennial sub-shrubs and herbs with a wide distribution in southern Africa (except J. dissecta in Sudan, Egypt and India). Plastid (rps16 and psbA-trnH) and nuclear (GScp) sequences were obtained for 42 species, mostly from the arid winter-rainfall west and southern regions of southern Africa. Applying both parsimony and Bayesian inference to combined molecular and morphological data sets, a phylogenetic hypothesis which is robust at the deeper nodes, was produced. This supports the monophyly of Jamesbrittenia, and also indicates the early divergence of J. ramosissima and three major clades.
- ItemOpen AccessPhylogenetics and biogeography of the relhanioid paper-daisy lineage (Asteraceae: Gnaphalieae) : palaeoenvironmental evolution, migration and speciation in southern Africa and the greater Afrotemperate regions(2014) Bentley, Joanne; Verboom, Tony; Bergh, NicolaThe true circumscription and subtribal division of Gnaphalieae is currently not known, and a series of recent molecular phylogenetic analyses have indicated that the previously-accepted subtribal delimitation of Anderberg (1991) comprises non-monophyletic entities (Bayer et al. 2000; Bergh & Linder 2009; Ward et al. 2009). Anderberg's (1991) morphological parsimony analysis identified five subtribes, including the largely southern African subtribe Relhaniinae, considered by Linder (2003) to be the tenth-largest “Cape Floral Clade”, as well as a non-classified group of taxa which he considered putatively “basal” to Gnaphalieae. A subsequent molecular analysis (Bayer et al. 2000) indicated that many of the taxa from Anderberg's (1991) subtribe Relhaniinae and the southern African members of the “basal taxa” constitute a single lineage. This lineage, termed the “Relhania clade” by Bergh & Linder (2009), is identified by several studies as the earliest-diverging lineage in Gnaphalieae (Bayer et al. 2000; Bergh & Linder 2009; Ward et al. 2009). The Relhania clade (whose members will hereafter also be referred to as “relhanioid” taxa) forms the focus of this thesis. To date, only placeholder representatives of relhanioid species have been represented in phylogenetic analyses (Bayer et al. 2000; Bergh & Linder 2009; Klaassen & Bergh 2012; Montes-Moreno et al. 2010; Smissen et al. 2011; Ward et al. 2009); thus the Relhania clade as currently defined comprises only 24 species. On morphological grounds, the following taxa are likely to be relhanioid: Antithrixia (monotypic), Arrowsmithia (monotypic), Athrixia (14 sp.), Comborhiza (ditypic), Leysera (3 sp.), Macowania (12 sp.), Nestlera (monotypic), Oedera (18 sp.), Oreoleysera (monotypic), Pentatrichia 4 (6 sp.), Phagnalon (41 sp.; three of which are subspecific), Relhania (13 sp.), Rhynchopsidium (2 sp.) and Rosenia (4 sp.). If all these taxa are confirmed to be members of the Relhania clade, the group will comprise a total of 119 species in 14 genera. Two further genera, Alatoseta (monotypic) and Philyrophyllum (ditypic) are believed to be closely-related to, if not members of, the Relhania clade (Anderberg 1991; Montes-Moreno et al. 2010) although they are morphologically anomalous taxa whose relationships are poorly understood.
- ItemOpen AccessPolyploid speciation in the Greater Cape Floristic Region : species limits within Ehrhara calycina(2013) Musker, Seth; Verboom, TonyEhrharta calycina J. E. Sm. (Poaceae) is a widespread and often abundant species whose core distribution lies within the Greater Cape Floristic Region (GCFR). Importantly, it shows a high degree of morphological and ploidy level variation. Based on observations of distinct forms co-occurring at multiple sites, the hypothesis that E. calycina comprises more than one species was tested. Morphological analysis of herbarium specimens using a multivariate approach found strong evidence for the presence of two distinct phenetic clusters among specimens from sites of sympatry, and these were termed ‘robust’ and ‘slender’ forms. This translated to a broader sampling of specimens from across the GCFR (n = 516), of which over 91% could be attributed to one or other form with >90% confidence using linear discriminant analysis. Importantly, chromosome counts supported the hypothesis that these phenetic clusters represent distinct cytotypes, with slender forms being diploid (n = 12) and robust forms tetraploid (n = 24), thus providing the primary reproductive isolating mechanism between the forms. Furthermore, differences in climatic niche suggest that these forms represent ecologically independent entities. Finally, evidence that the forms differ in palatability has considerable practical implications given that E. calycina is regarded as having high pasture value. Together, our results provide multiple lines of evidence for the existence of at least two morphologically distinct, reproductively isolated species within E. calycina, and suggest that the role of polyploidy in generating floral diversity in the GCFR may be more important than previously thought.
- ItemOpen AccessThe spatial and temporal dynamics of diversification in Tylecodon, Cotyledon and Adromischus (Crassulaceae) in southern Africa(2008) Nowell, Tracey L; Verboom, Tony; Midgley, Jeremy JA molecular phylogenetic hypothesis was generated for Tylecodon, Cotyledon and Adromischus in order to estimate the timing and spatial dynamics of diversification across these three southern African genera. These data were used to investigate the correlates and consequences of adaptations to extreme aridity and summer drought in members of the group.
- ItemOpen AccessSpecies delimitation and speciation process in the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae) in South Africa(2019) Shaik, Zaynab; Verboom, Tony; Bergh, Nicola G.The remarkable richness of the Cape Floristic Region (CFR) and the high in situ diversification inferred for the region prompt interest in two key areas: first, to what extent has the true species richness of the Cape been discovered and described, and second, what are the key drivers of speciation? Steady efforts in taxonomy dating back to the early 17th century have led some to estimate that over 99% of species in the Cape flora have already been described. However, taxonomic research in the Cape has, as elsewhere, relied on morphology for delimiting species, implying that undiscovered species diversity among cryptic taxa may be substantial. Early ideas regarding the drivers of diversification in the Cape flora emphasised climatically-induced vicariant speciation. Since that time, both vicariance and ecological speciation have been invoked as drivers of diversification. However, the relative contributions of either of these modes to the richness of the flora remains unclear. The present work focuses on Seriphium plumosum, a species complex in the daisy tribe Gnaphalieae with a recent evolutionary origin and a core distribution in the Cape Floristic Region. The species’ problematic taxonomic history, its substantial morphological and ecological variability, as well as its large geographic distribution in southern Africa suggest that the current concept of the species houses multiple independent evolutionary species. Species limits within the complex are reevaluated using the Bayes Factor Delimitation method of Leaché et al. (2014) within an integrative taxonomic approach, incorporating evidence from next-generation DNA sequence data, previous taxonomic treatments, morphology, ecology and geographic distribution. The drivers of lineage divergence are then investigated at the population level within selected species in the group, with a focus on neutral and adaptive processes, and the spatial contexts within which each of these processes is thought to operate. The evidence presented here provides support for ten or eleven independent evolutionary species housed within the current concept of S. plumosum. The species currently considered sibling to the complex, Seriphium cinereum, is strongly supported as embedded within the complex, which I thus term the S. plumosum clade. In order to better facilitate identification of the species, several of the evolutionary species uncovered are consolidated. As such, a total of nine species are described in the taxonomic treatment of the clade, each of which is morphologically and ecologically cohesive, and five of which qualify as biological species sensu Mayr (1969). These include S. plumosum1 and S. cinereum under new circumscriptions, four new species; Seriphium alto-argillaceum, S. burrowsii, S. crypticum and S. dunensis, and three species housed within the current concept of S. plumosum and formerly treated within Stoebe; Seriphium burchellii Levyns, S. vulgaris Levyns, and S. virgatum Thunb. At the population level within selected species in the S. plumosum clade, neutral processes and weak divergent selection within a spatially discontinuous context are supported as the key driver of differentiation. These findings suggest that phylogenetic niche conservatism and/or the limited dispersal abilities characteristic of many Cape clades have been important in diversification by neutral and adaptive processes in the region. If extrapolatable to other Cape lineages, this work implies that undiscovered species diversity in the Cape may considerably exceed recent estimates, and that the role of non-adaptive processes in generating species diversity may be considerably underestimated.