Browsing by Author "Dreyer, Leanne L."
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- ItemConsistent phenological shifts in the making of a biodiversity hotspot : the Cape flora(BioMed Central, 2011-02) Warren, Ben H.; Bakker, Freek T.; Bellstedt, Dirk U.; Bytebier, Benny; Claszen-Bockhoff, Regine; Dreyer, Leanne L.; Edwards, Dawn; Forest, Felix; Galley, Chloe; Hardy, Christopher R.; Linder, H. Peter; Muasya, A. Muthama; Mummenhoff, Klaus; Oberlander, Kenneth C.; Quint, Marcus; Richardson, James E.; Savolainen, Vincent; Schrire, Brian D.; Van der Niet, Timotheus; Verboom, G. Anthony; Yesson, Christopher; Hawkins, Julie A.ABSTRACT: Background: The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results: Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions: Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.
- ItemGenome sequences of Knoxdaviesia capensis and K. proteae (Fungi: Ascomycota) from Protea trees in South Africa(BioMed Central, 2016) Aylward, Janneke; Steenkamp, Emma T.; Dreyer, Leanne L.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J.Two closely related ophiostomatoid fungi, Knoxdaviesia capensis and K. proteae, inhabit the fruiting structures of certain Protea species indigenous to southern Africa. Although K. capensis occurs in several Protea hosts, K. proteae is confined to P. repens. In this study, the genomes of K. capensis CBS139037 and K. proteae CBS140089 are determined. The genome of K. capensis consists of 35,537,816 bp assembled into 29 scaffolds and 7940 predicted protein-coding genes of which 6192 (77.98 %) could be functionally classified. K. proteae has a similar genome size of 35,489,142 bp that is comprised of 133 scaffolds. A total of 8173 protein-coding genes were predicted for K. proteae and 6093 (74.55 %) of these have functional annotations. The GC-content of both genomes is 52.8 %.
- ItemIMA Genome-F 11: Draft genome sequences of Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis and genome annotation for Ceratocystis fimbriata(BMC (part of Springer Nature), 2019-09-13) Wingfield, Brenda D.; Fourie, Arista; Simpson, Melissa C.; Bushula-Njah, Vuyiswa S.; Aylward, Janneke; Barnes, Irene; Coetzee, Martin P. A.; Dreyer, Leanne L.; Duong, Tuan A.; Geiser, David M.; Roets, Francois; Steenkamp, E. T.; Van Der Nest, Magriet A.; van Heerden, Carel J.; Wingfield, Michael J.ENGLISH ABSTRACT: Draft genomes of the fungal species Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis are presented. In addition an annotation of the genome of Ceratocystis fimbriata is presented. Overall these genomes provide a valuable resource for understanding the molecular processes underlying pathogenicity and potential management strategies of these economically important fungi.
- ItemKnoxdaviesia proteae is not the only Knoxdaviesia-symbiont of Protea repens(International Mycological Association, 2015-11-10) Aylward, Janneke; Dreyer, Leanne L.; Steenkamp, Emma T.; Wingfield, Michael J.; Roets, FrancoisTwo polyphyletic genera of ophiostomatoid fungi are symbionts of Proteaceae in southern Africa. One of these, Knoxdaviesia, includes two closely related species, K. proteae and K. capensis, that have overlapping geographical distributions, but are not known to share Protea host species. Knoxdaviesia capensis appears to be a generalist that occupies numerous hosts, but has never been found in P. repens, the only known host of K. proteae. In this study, extensive collections were made from P. repens and isolates were identified using DNA sequence comparisons. This led to the surprising discovery of K. capensis from P. repens for the first time. The fungus was encountered at a low frequency, suggesting that P. repens is not its preferred host, which may explain why it has not previously been found on this plant. The basis for the specialisation of K. proteae and K. capensis on different Protea species remains unknown.
- ItemMonitoring the success of an old-field rehabilitation trial in the winter rainfall succulent Karoo : the effect of Oxalis pes-caprae(Stellenbosch : University of Stellenbosch, 2004-12) Ghebremariam, Ghirmai Emun; Esler, Karen Joan; Dreyer, Leanne L.; University of Stellenbosch. Faculty of Agrisciences. Dept. of Conservation Ecology and Entomology.ENGLISH ABSTRACT: The main aim of an old field rehabilitation trial initiated in 2000 was to find a solution to the rehabilitation process for approximately 90 000 ha of unutilised land in the Little Karoo, South Africa. Depending only on a natural succession process to restore unutilised old fields would mean that the period of recovery would be longer than the life span of an average farmer. The trial, initiated by Witbooi in 2000 aimed to see how human intervention can facilitate the process of rehabilitation of old-fields. Three years later, the trial was again monitored to evaluate the success of reseeded indigenous species and method of cultivation in the rehabilitation process. A second objective was based on a result of Witbooi (2002) who showed that there was a tendency of 0. pes-caprae to invade disturbed areas, and aimed to evaluate the effect of this species on the rehabilitation process. Seven indigenous species were reseeded in 2000, of which only four species germinated and survived to the present. These surviving species are Pteronia incana Burm Dc., Tripteris sinuata DC., Ehrharta calycina SM and Chaetobromus dregeanus Nees. The highest level of recruitment in 2001 was recorded for T sinuata followed by P. incana, E. calycina and C. dregeanus. In September 2003, three years after the trial was initiated, the highest number of surviving seedlings were of T sinuata followed by E. calycina, C. dregeanus and P. incana. Five different cultivation methods were used to enhance the germination rate and survival of seedlings. The number of seedlings that survived differs according to the cultivation methods and soil type. Tripteris sinuata had the highest number of surviving seedlings in all cultivation methods off-heuweltjies. Tripteris sinuata was therefore selected to analyse the effect of various cultivation methods. The second objective was to study the impact of Oxalis pes-caprae on species diversity in restored old fields by assessing its ability to disperse in old fields under different cultivation methods. The multivariate ANOVA results showed that there was a significant difference in the density of O. pes-caprae between on and off heuweltjies (sites) and treatments (cultivation methods). There was a significant difference in the density of O. pes-caprae between cultivation methods. A Post Hoc LSD test showed a significant difference in the density of aboveground O. pes-caprae plants between control sites (no disturbance) compared to those sites that underwent some sort of soil disturbance. There was, however, no significant difference in the abundance of O. pes-caprae on plots that underwent some sort of disturbance (i.e Cleared vs Tilled vs Disked vs Ploughed sites) on heuweltjies. There was a significant difference in the number of O. pes-caprae bulbs collected between blocks (on and off-heuweltjie) and significant differences between cultivation methods. There was also a significant difference in bulb diameter between cultivation methods when compared between on and off-heuweltjie sites. The bulbs were classified into four measurement classes. The highest number of small (2-5 mm diameter) and medium (5-8 mm diameter) sized bulbs were found in the Tilled cultivation method. In contrast the Control treatment (uncultivated) had the highest number of large sized bulbs (14-17 mm diameter) and medium bulbs size categories. In conclusion, T. sinuafa has the potential to be used for rehabilitation of old fields in combination with Tilled cultivation method. Attention should be paid to the effect of O. pes-caprae especially on heuweltjies where this species showed a complete dominance in the rehabilitation trial.
- ItemNitrogen-fixing bacteria and Oxalis – evidence for a vertically inherited bacterial symbiosis(BMC (part of Springer Nature), 2019-10-23) Jooste, Michelle; Roets, Francois; Midgley, Guy F.; Oberlander, Kenneth C.; Dreyer, Leanne L.Background: Plant-endophyte symbioses often revolve around nitrogen metabolism, and involve varying degrees of intimacy. Although evidence for vertical inheritance of nitrogen-fixing endophytic bacteria is increasing, it is confined mostly to crop plants, and to date no such system has been reported for geophytes. Methods: Bacterial endophytes associated with Oxalis, the most species-rich geophytic genus form the Cape Flora in southern Africa was studied. Culturable endophytes were isolated from surface-sterilized vegetative and reproductive plant organs for six host species at three locations. Colonies of microbes on various artificial media were morphotyped, enumerated and identified using sequence data. Filter exclusion experiments were conducted to determine if endophytes were vertically transmitted to seeds, determine if mucilage plays a role to actively attract microbes from the soil and to assess microbial richness isolated from the mucilage of Oxalis seedlings. Fluorescent microscopy was implemented in order to visualize endophytic bacteria in cryo-sectioned seeds. Results: Evidence for a novel, vertically transmitted symbiosis was reported. Communities of nitrogen-fixing and plant growth-promoting Bacillus endophytes were found to associate with selected Oxalis hosts from nitrogen-deficient environments of the Cape. Bacillus endophytes were ubiquitous and diverse across species and plant bodies, and were prominent in seeds. Three common nitrogen-fixing Bacillus have known oxalotrophic properties and appear to be housed inside specialised cavities (containing oxalates) within the plant body and seeds. Conclusions: The discovery of vertical transmission and potential benefits to both host and endophyte suggest a particularly tight mutualism in the Oxalis-endophyte system. This discovery suggests unexpected ways in which geophytes might avoid nitrogen deficiency, and suggest that such symbioses are more common than previously expected.
- ItemNomenclatural notes on southern African Oxalis species(AOSIS, 2018) Dreyer, Leanne L.; Oberlander, Kenneth C.; Klopper, Ronell R.Background: The correct author citation of Oxalis sonderiana (Kuntze) J.F.Macbr. and the validity and identity of the species Oxalis beneprotecta R.Knuth, Oxalis bullulata T.M.Salter and Oxalis pulchella Jacq. var. beneprotecta (R.Knuth) T.M.Salter are unclear. Objectives: To resolve the nomenclatural and taxonomic confusion surrounding these four taxa. Method: We studied relevant herbarium records (especially type material) of all the taxa, and paired this with scrutiny of all publications that bear reference to the nomenclature and taxonomy of these species. Results: The correct author citation for Oxalis sonderiana has been determined; Oxalis bullulata is confirmed as a distinct species, and the continued recognition of Oxalis beneprotecta as a variety of Oxalis pulchella is suggested. It is further ascertained that the name ‘Oxalis nidulans Turcz.’ is not a later homonym, but a reference to a misapplication of Oxalis nidulans Eckl. & Zeyh. to the type specimen of Oxalis sonderiana. Conclusion: These results clarify the current confusion surrounding these taxa in global herbaria and in national and international databases.
- ItemOxalis seeds from the Cape Flora have a spectrum of germination strategies(Botanical Society of America, 2019) Jooste, Michelle; Midgley, Guy F.; Oberlander, Kenneth C.; Dreyer, Leanne L.PREMISE OF THE STUDY: Seed germination strategy has profound ecological and evolutionary consequences, with transitions between germination strategies receiving renewed recent attention. Oxalis from the Cape Flora, South Africa, has seeds with two contrasting germination strategies: orthodox and recalcitrant. The morphological gulf between these strategies (and potential intermediate morphologies) has been poorly quantified, with questions regarding their ecological function and evolution. We reconsidered this binary classification, emphasizing potential intermediate states. METHODS: Seed physiological traits were used to assign strategies to 64 Oxalis species. We tested for morphological/phenological signal corresponding to defined strategies with cluster, principal component, Kmeans clustering and discriminant analyses. KEY RESULTS: We show that an intermediate germination strategy does exist among Cape Oxalis, with two possible morphological groups within each strategy. These could reflect a continuum of germination states, where an ancestral orthodox strategy evolved towards a maximally recalcitrant peak, with a mosaic of intermediate states reflected in extant taxa. CONCLUSIONS: Environmental factors may affect germination strategy and distribution throughout the Cape because recalcitrant and intermediate species are confined to the winter rainfall region. They occupy specialized niches and may face adverse impacts under predicted climate change (hotter and drier winters), meriting focused future conservation.
- ItemPanmixia defines the genetic diversity of a unique arthropod-dispersed fungus specific to Protea flowers(Wiley Open Access, 2014-09) Aylward, Janneke; Dreyer, Leanne L.; Steenkamp, Emma T.; Wingfield, Michael J.; Roets, FrancoisKnoxdaviesia proteae, a fungus specific to the floral structures of the iconic Cape Floral Kingdom plant, Protea repens, is dispersed by mites phoretic on beetles that pollinate these flowers. Although the vectors of K. proteae have been identified, little is known regarding its patterns of distribution. Seed bearing infructescences of P. repens were sampled from current and previous flowering seasons, from which K. proteae individuals were isolated and cultured. The genotypes of K. proteae isolates were determined using 12 microsatellite markers specific to this species. Genetic diversity indices showed a high level of similarity between K. proteae isolates from the two different infructescence age classes. The heterozygosity of the population was high (0.74 +- 0.04), and exceptional genotypic diversity was encountered (^G = 97.87%). Population differentiation was negligible, owing to the numerous migrants between the infructescence age classes (Nm = 47.83) and between P. repens trees (Nm = 2.96). Parsimony analysis revealed interconnected genotypes, indicative of recombination and homoplasies, and the index of linkage disequilibrium confirmed that outcrossing is prevalent in K. proteae (rd = 0.0067; P = 0.132). The high diversity and panmixia in this population is likely a result of regular gene flow and an outcrossing reproductive strategy. The lack of genetic cohesion between individuals from a single P. repens tree suggests that K. proteae dispersal does not primarily occur over short distances via mites as hypothesized, but rather that longdistance dispersal by beetles plays an important part in the biology of these intriguing fungi.
- ItemThe phylogenetic significance of leaf anatomical traits of southern African oxalis(BioMed Central, 2016-10) Jooste, Michelle; Dreyer, Leanne L.; Oberlander, Kenneth C.Background: The southern African Oxalis radiation is extremely morphologically variable. Despite recent progress in the phylogenetics of the genus, there are few morphological synapomorphies supporting DNA-based clades. Leaflet anatomy can provide an understudied and potentially valuable source of information on the evolutionary history and systematics of this lineage. Fifty-nine leaflet anatomical traits of 109 southern African Oxalis species were assessed in search of phylogenetically significant characters that delineate clades. Results: A combination of 6 leaflet anatomical traits (stomatal position, adaxial epidermal cells, abaxial epidermal cells, mesophyll, sheath around vascular tissue, degree of leaflet conduplication) clearly support various clades defined by previous DNA-based phylogenetic work. Other, mostly continuous leaflet anatomical traits were highly variable and showed less phylogenetic pattern. Conclusions: Major and unexpected findings include the transition from ancestral hypostomatic leaflets to adaxially-located stomata in the vast majority of southern African Oxalis, the loss of semi-swollen AB epidermal cells and the gain of swollen adaxial and abaxial epidermal cells in selected clades, and multiple changes from ancestral bifacial mesophyll to isobilateral or homogenous mesophyll types. The information gathered in this study will aid in the taxonomic revision of this speciose member of the Greater Cape Floristic Region and provide a basis for future hypotheses regarding its radiation.
- ItemA plant pathology perspective of fungal genome sequencing(International Mycological Association, 2017) Aylward, Janneke; Steenkamp, Emma T.; Dreyer, Leanne L.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J.The majority of plant pathogens are fungi and many of these adversely affect food security. This minireview aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.
- ItemTeratosphaeria stem canker of Eucalyptus : two pathogens, one devastating disease(British Society for Plant Pathology, 2018) Aylward, Janneke; Roets, Francois; Dreyer, Leanne L.; Wingfield, Michael J.Background: Teratosphaeria gauchensis and T. zuluensis are closely related fungi that cause Teratosphaeria (previously Coniothyrium) stem canker disease on Eucalyptus species propagated in plantations for commercial purposes. This disease is present in many countries in which Eucalyptus trees are planted, and continues to spread with the international trade of infected plant germplasm. Taxonomy: Fungi, Ascomycota, Pezizomycotina, Dothideomycetes, Dothideomycetidae, Capnodiales, Teratosphaeriaceae, Teratosphaeria. Identification: The causal agents form dark masses of pycnidia that are visible on the surface of distinct stem cankers that typically form on young green stem tissues. Accurate diagnosis of the causal agents requires DNA sequence data. Host range: Nine species of Eucalyptus are known to be affected. Of these, E. grandis and its hybrids, which include some of the most important planting stock globally, appear to be particularly vulnerable. Disease symptoms: Small necrotic lesions develop on young green stem tissue. These lesions coalesce to form large cankers that exude gum. Epicormic shoots develop below the girdling canker and, in severe cases, trees die.