Phylogenetic and functional growth from diversification in the Cape grass genus Ehrharta Thunb

Includes bibliography.This thesis uses phylogenetic and comparative data to test an hypothesis of adaptive radiation in the Cape grass genus Ehrharta Thunb. sensu stricto. Morphological data and sequence data from two noncoding regions of DNA (lTS1 and trnL-F) are used to produce a phylogenetic hypothesis for the tribe Ehrharteae. Combined analysis of these data sets resolves four principal clades that approximate the genera Ehrharta s. s., Micro/aena, Tetrarrhena and Zotovia and this result thus supports a four-genus classification. Poor resolution and a reduction in branch length at the base of a clade nested within Ehrharta s. s. suggests past radiation. Parsimony-based reconstruction of ancestral habitats and growth form attributes indicates that such radiation is associated with a historical transition to seasonallydrier but more fertile habitats, and the coincident or subsequent evolution of several growth form novelties (e.g. buried and swollen culm bases and annualness). These traits are interpreted to reflect divergent strategies for surviving seasonal drought (Le. via seed or storage). Much higher transpiration rates in summer-deciduous leaves than in perennating culms of two species suggest that the evolution of summer-deciduous foliage was important in the occupation of seasonally-arid habitats. Controlled growth experiments are used to test the hypothesis that divergence in persistence traits is associated with differences in seedling biomass allocation and relative growth rate (RGR). Ehrharta s. s. shows wide variation in seedling RGR and regressions based on phylogenetically independent contrasts suggest that differences are better explained by early biomass allocation than leaf area indices. Species with a high allocation to leaves grow faster and flower sooner, so these traits are typical of seeding species

Distribution quantitative morphological variation and preliminary molecular analysis of different growth forms of wild rooibos (Aspalathus linearis) in the northern Cederberg and on the Bokkeveld Plateau

Aspalathus linearis (Fabaceae) is endemic to the Cape Floristic Region in the Western Cape and Northern Cape Provinces of South Africa. The reddish leaves and stems, primarily of one cultivar, are used to make a commercially important tea which is marketed locally and internationally as ‘rooibos’ or ‘redbush’ tea. In historical times rooibos was collected in the wild. In the twentieth century cultivation of a single cultivar increasingly replaced wild harvest to meet growing demand. Recently, tea from wild forms of the species, which vary significantly in growth form and reproductive strategy, has been marketed by small-scale farmers in Wupperthal and on the Suid Bokkeveld plateau in the northern part of the species' distribution. Little information on the wild forms of this species has been published, although a rich body of knowledge exists amongst local harvesters and other land-users. In this study, we focus on the northern part of the species’ distribution area where wild rooibos is harvested for commercial sale to niche organic and fair-trade markets. We adopt a transdisciplinary approach to (1) document the different growth forms, (2) develop a bioclimatic model of the potential distribution of the species, (3) quantify the morphological variation that exists between growth forms relative to the established cultivar and (4) use molecular techniques to provide a preliminary insight into the infraspecific diversity of different wild A. linearis growth forms. Our results show that local land users in the region identify four main growth forms of wild A. linearis. These are an ‘erect form’ and a ‘prostrate form’ in the Wuppertal area, a ‘shrub form’ in the Suid Bokkeveld, and a ‘tree form’ that has been observed at specific sites at Wupperthal, Biedouw and the Suid Bokkeveld. The PCA analysis of seven morphological traits identified three growth forms, which support the land user descriptions except in the case of the 'tree' and 'erect' forms which co-occurred in coordinate space. Both shrub and prostrate forms are wider than they are taller and possess more stems closer to the ground than erect forms. While the stems of both shrub and prostrate forms lie relatively flat on the ground, stem thickness is significantly greater in shrub forms. The tree type, the erect form and the cultivar studied possess the highest harvestable biomass. Prostrate forms and shrub forms resprout after fire while erect and tree forms regenerate from seed only. Haplotypic variation was assessed using DNA sequences from a single chloroplast region and revealed strong genetic differences between the different growth forms. Although preliminary, there is some evidence that sprouting and nonsprouting forms of the species are genetically isolated. This has important taxonomic implications for the species. Additional chloroplast regions and a nuclear region were also identified as variable and potentially useful markers for a multi-locus molecular approach to studying taxonomic and ecological questions within the species

Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma

Burkitt lymphoma (BL) is responsible for many childhood cancers in sub-Saharan Africa, where it is linked to recurrent or chronic infection by Epstein-Barr virus or Plasmodium falciparum. However, whether human leukocyte antigen (HLA) polymorphisms, which regulate immune response, are associated with BL has not been well investigated, which limits our understanding of BL etiology. Here we investigate this association among 4,645 children aged 0-15 years, 800 with BL, enrolled in Uganda, Tanzania, Kenya, and Malawi. HLA alleles are imputed with accuracy >90% for HLA class I and 85-89% for class II alleles. BL risk is elevated with HLA-DQA1*04:01 (adjusted odds ratio [OR] = 1.61, 95% confidence interval [CI] = 1.32-1.97, P = 3.71 × 10-6), with rs2040406(G) in HLA-DQA1 region (OR = 1.43, 95% CI = 1.26-1.63, P = 4.62 × 10-8), and with amino acid Gln at position 53 versus other variants in HLA-DQA1 (OR = 1.36, P = 2.06 × 10-6). The associations with HLA-DQA1*04:01 (OR = 1.29, P = 0.03) and rs2040406(G) (OR = 1.68, P = 0.019) persist in mutually adjusted models. The higher risk rs2040406(G) variant for BL is associated with decreased HLA-DQB1 expression in eQTLs in EBV transformed lymphocytes. Our results support the role of HLA variation in the etiology of BL and suggest that a promising area of research might be understanding the link between HLA variation and EBV control

An investigation of character variation in Chaetobromus Nees (Danthonieae: Poaceae) in relation to taxonomic and ecological pattern

Character variation in Chaetobromus, a genus of palatable grasses endemic to the arid western areas of southern Africa, was used to derive a classification reflecting taxonomic and ecological pattern. The present study differs from earlier biosystematic investigations by its much more intensive approach to sampling, with 75 anatomical, morphological and cytological characters and 169 individual samples being used. The use of larger population samples permitted quantification of variation within populations, in addition to that among populations and groups. Phenetic methods revealed the existence of three groups, approximating three formerly described taxa and reflecting divergent ecological strategies in Chaetobromus. A lack of diagnostic field characters argues against their recognition at species level, and Chaetobromus Nees is here described as monotypic, the type species, C. involucratus (Schrad.) Nees, comprising three subspecies C. involucratus subsp. involucratus, C. involucratus subsp. villosus Verboom and C. involucratus subsp. dregeanus (Nees) Verboom. There is overlap among subspecies in most characters although many showed significant mean differences. Within subspecies, character variation appears to be homogeneously distributed with respect to population boundaries suggesting that these are likely to have little impact on sampling. An investigation testing the effect of sample strategy on variation capture and taxonomic group detection suggests that a sample of 10-15 specimens is likely to account for most variation present. Phylogenetically, Chaetobromus is included in the tribe Danthonieae, and, on morphological evidence, is probably basal to a clade containing Pentaschistis, Pentameris and Pseudopentameris. The genus appears to occupy a niche unique among the African danthonioids, favouring lime-rich, basic soils and a strongly-seasonal winter-rainfall regime with arid summers. Ecological differences among the subspecies are reflected in differences in growth form and vegetative and reproductive phenologies. The niche requirements of Chaetobromus may be adequately specific to explain the patchy distribution of the genus. Bibliography: pages 119-131

Data from: Specialization to extremely low-nutrient soils limits the nutritional adaptability of plant lineages

Specialization to extreme selective situations promotes the acquisition of traits whose coadaptive integration may compromise evolutionary flexibility and adaptability. We test this idea in the context of the foliar stoichiometry of plants native to the South African Cape. Whereas foliar concentrations of nitrogen, phosphorus (P), potassium (K), calcium, magnesium, and sodium showed strong phylogenetic signal, as did the foliar ratios of these nutrients to P, the same was not true of the corresponding soil values. In addition, although foliar traits were often related to soil values, the coefficients of determination were consistently low. These results identify foliar stoichiometry as having a strong genetic component, with variation in foliar nutrient concentrations, especially [P] and [K], being identified as potentially adaptive. Comparison of stoichiometric variation across 11 similarly aged clades revealed consistently low foliar nutrient concentrations in lineages showing specialization to extremely low-nutrient fynbos heathlands. These lineages also display lower rates of evolution of these traits as well as a reduced tendency for foliar [P] to track soil [P]. Reduced evolutionary lability and adaptability in the nutritional traits of fynbos-specialist lineages may explain the floristic distinctness of the fynbos flora and implies a reduced scope for edaphically driven ecological speciation

R files

Zip archive containing the R code and associated input files used for the main analyses

beast_revised_mcc_newick

BEAST maximum clade credibility tree used for comparative analyses

TableS2

Spreadsheet scoring (present = 1, absent = 0) the vegetation (columns 5-9) and geological (columns 10-14) associations of study species. The final two columns indicate the total number of vegetation types and geologies occupied by each species