Ceratocystis fimbriata is the type species for the genus Ceratocystis and was first described as the causal agent of black rot in sweet potatoes. However, evidence from DNA sequence data suggests that C. fimbriata is in fact a species complex (C. fimbriata sensu lato) consisting of many morphologically similar cryptic species. Species in this complex are pathogens of important root and fruit crops and trees in the forestry industry world-wide. Population studies on some of these species have mainly relied on microsatellite markers. However, nothing is known regarding the microsatellite structure within Ceratocystis species or any species in the order Microascales in which Ceratocystis resides. The need for a more robust identification tool is also required to differentiate between species in this complex. The first chapter of this thesis provides a review of the literature on microsatellite markers, particularly in fungi. It also discusses the history of microsatellites, mechanisms of microsatellite evolution and functional importance in selected fungal examples. In addition, isolation methodologies are compared and contrasted to newly developed techniques that include bioinformatic searches of genome sequences. Opportunities to use and develop microsatellite markers in Ceratocystis species is also discussed with an emphasis on the possibilities that more microsatellites markers would provide. Microsatellites are abundant in eukaryotic genomes, and fungi are no exception. Analyses of microsatellite content in eukaryotic and fungal genomes have shown that fungi contain fewer microsatellites and that each organism shows preference for particular motifs. In Chapter 2 of this thesis, the abundance and distribution of microsatellites in the recently sequenced C. fimbriata genome is investigated. Comparisons to other fungi and eukaryotes show that C. fimbriata follows the general pattern of microsatellite structure, however it is unique in its preference for certain motifs. The C. fimbriata sensu lato species complex contains morphologically indistinct species. Microsatellite markers previously developed for a population study could differentiate between some of the cryptic species based on their geographic location and host-specificity. In Chapter 3 a subset of microsatellite markers identified in gene regions in Chapter 2 are used to develop a diagnostic test to differentiate between species in the complex. Microsatellite markers that are polymorphic between species but monomorphic within species were selected for this purpose. However, not all species could be distinguished using this diagnostic test. This thesis is presented as a series of chapters in which Chapters 3 2 and 3 are in manuscript format. Consequently each chapter represents an independent article and repetition between these chapters has been unavoidable. / Dissertation (MSc)--University of Pretoria, 2014. / Genetics / Unrestricted

Leishmania tropica ist der Auslöser von kutaner Leishmaniose beim Menschen und kommt in Afrika über den Mittleren Osten bis nach Nordindien vor. Mittels Mikrosatellitentypisierung (MLMT) wurde die weltweite Populationsstruktur dieser Spezies und der nahe verwandten Spezies L. aethiopica aufgedeckt, indem sowohl Methoden angewandt wurden, die auf genetischen Distanzen beruhen als auch solche, die auf der Analyse von Allelfrequenzen basieren. Die 195 Stämme von L. tropica sowie die acht Stämme von L. aethiopica gruppierten hauptsächlich gemäß ihrer geographischen Herkunft. Die Stämme von L. aethiopica stellten eine eigene Gruppe dar, die allerdings innerhalb der afrikanischen Stämme von L. tropica gruppierte. Vorläufige Ergebnisse einer genomweiten SNP-Analyse haben die Ergebnisse der Mikrosatellitenanalyse weitgehend bestätigt. Um die Gründe für die hohe genetische Variabilität innerhalb der Spezies L. tropica herauszufinden, wurde eine Funktionelle Klonierung durchgeführt, in der N-methyl-N’-nitro-N-nitrosoguanidin (MNNG) als Indikator für ein funktionierendes oder eingeschränktes Mismatch Repair (MMR)-System eingesetzt wurde. Dafür wurde ein Akzeptorstamm (hohe MNNG-Toleranz) mit einer Cosmidbibliothek, die genomische DNA eines Donorstammes (niedrige MNNG-Toleranz) enthielt, transfiziert. Die erhaltenen Transfektanten wurden dann auf ihre MNNG-Toleranz getestet. Die zeit- und kosteneffiziente Identifizierung von großen Mengen an Sandmücken ist wichtig für Feldstudien, in denen mehrere Tausend Mücken gefangen werden. Hier wird eine multiplexe Technik zur ligationsabhängigen Sondenamplifizierung vorgestellt, die die Identifizierung von Sandmücken-Spezies im Mittleren Osten ermöglicht. Die Spezies Phlebotomus syriacus, P. arabicus und P. papatasi können durch diese Methode mit spezies-spezifischen Sonden eindeutig identifiziert werden. Außerdem kann diese Methode dazu genutzt werden, weitere Spezies zu diskriminieren und auf gepoolte Sandmücken angewandt werden. / Leishmania tropica is the causative agent of human cutaneous leishmaniasis in foci ranging from Africa through the Middle East to northern India. By multilocus microsatellite typing (MLMT), the world-wide population structure of this species and its closely related species L. aethiopica has been revealed applying methods based on both genetic distances and allele frequencies. The 195 strains of L. tropica and eight strains of L. aethiopica largely clustered according to their geographical origins. The strains of L. aethiopica formed a distinct group, although clustering among other African strains of L. tropica. Preliminary data obtained through a whole genome sequencing approach including strains of L. tropica, L. aethiopica and L. major have largely corroborated the results of the MLMT approach. To reveal the reasons for the high genetic variability among strains of L. tropica, a Functional Cloning approach was conducted using N-methyl-N’-nitro-N-nitrosoguanidin (MNNG) as an indicator for a functioning or impaired mismatch repair (MMR) system. The transfectants retrieved from the transfection of an acceptor strain exhibiting high MNNG tolerance with a cosmid library bearing the genomic DNA of a donor strain with a reduced MNNG tolerance were screened for the restored phenotype of the donor strain. The time- and cost-efficient identification of a large amount of sand flies is important since several thousands are caught during field studies. Here, a multiplex ligation-dependent probe amplification approach (MLPA) for the identification of sand flies endemic to the Middle East is introduced. The unambiguous identification of Phlebotomus syriacus, P. arabicus and P. papatasi was possible with this approach using species-specific probes. Furthermore, this technique has the potential to discriminate more species and to be applied to pooled sand fly specimens.

The data from public herbal collections were used to determine the frequency of the occurence of fertile bracken populations. Samples of bracken were collected to assess the degree of fertility and also to reveal the frequency of both diploid and triploid cytotypes using flow cytometry. Collected samples were also used for SSR analysis to characterize the population structure of both cytotypes and the propagation of triploid plants of bracken.

Triops cancriformis (Crustacea: Notostraca) occurs in ephemeral habitats like rain pools or floodplain pools distributed over a large geographical range. The named habitats are disturbed by human impacts and, consequently, T. cancriformis is endangered throughout its distribution range. In the present thesis the populated habitats and threats are characterised and further morphological and genetic variations detected among and within European populations are reported. On the basis of recent investigations it is shown that T. cancriformis subspecies separation is hampered by an individual variability which points to the necessity of species revision. The analysis of mitochondrial gene sequence data suggests that the species has colonised most of Europe very recently. The advantage of a complex reproductive strategy in T. cancriformis in this process is discussed. The population structure resolved with nuclear DNA markers highlights that there is low allelic diversity among and within populations compared to other Branchiopoda (Daphnia). By means of the present study it can be shown that habitat conservation is most important to protect T. cancriformis.

Triops cancriformis (Crustacea: Notostraca) occurs in ephemeral habitats like rain pools or floodplain pools distributed over a large geographical range. The named habitats are disturbed by human impacts and, consequently, T. cancriformis is endangered throughout its distribution range. In the present thesis the populated habitats and threats are characterised and further morphological and genetic variations detected among and within European populations are reported. On the basis of recent investigations it is shown that T. cancriformis subspecies separation is hampered by an individual variability which points to the necessity of species revision. The analysis of mitochondrial gene sequence data suggests that the species has colonised most of Europe very recently. The advantage of a complex reproductive strategy in T. cancriformis in this process is discussed. The population structure resolved with nuclear DNA markers highlights that there is low allelic diversity among and within populations compared to other Branchiopoda (Daphnia). By means of the present study it can be shown that habitat conservation is most important to protect T. cancriformis.