Having outlined the present situation as regards rival taxonomic philosophies, and some of its historical background, the thesis examines this attempt to recategorize taxa as individual-like entities, and finds it wanting. The properties of species which render them regardable as individuals do not readily extend to more inclusive levels, or, if they do, are not readily restricted solely to cladistic taxa. Cladistic systematization, in moving away from the notion of a taxon as a class of similar entities, may cease to convey the information expected of a classification system. The practice of biology requires a more flexible and more stable taxonomy than can be provided by strict adherence to cladistic rules, and taxa are-better regarded as 'historical classes', delineated neither by pure unanalysed similarity nor by logical transformation of hypotheses of phylogenetic relationship, but by a considered pragmatic synthesis of the two, employing the notion of convexity as a criterion of acceptability.

Thesis (Ph. D.)--University of Hawaii at Manoa, 1995. / Includes bibliographical references (leaves 174-199). / Microfiche. / xiv, 199 leaves, bound ill. (some col.) 29 cm

Thesis--City University of New York. / Bibliography: p. 327-340.

Thesis (Ph.D.) -- University of Rhode Island, 2009. / Typescript. Includes bibliographical references (leaves 351-371).

Thesis (M.S.)--Rochester Institute of Technology, 2007. / Typescript. Includes bibliographical references (leaves 146-149).

Kniphofia, a genus of approximately 71 species, is almost entirely African with two species occurring in Madagascar and one in Yemen. Commonly known as ‘red hot pokers’ they are popular among horticulturists. The genus is also well known for its complex alpha taxonomy. To date, no studies have examined the phylogenetic relationships among species or the evolutionary history of the genus, and little work has been done on their biogeography. The main focus of this study was (i) to review the alpha taxonomy, (ii) to assess diversity and endemism in Kniphofia, (iii) to use DNA sequence data to reconstruct a specieslevel phylogeny to understand intra-generic species relationships and evolutionary processes (iv) to use phylogeographic approaches to study the biogeography and evaluate biogeographical patterns, and (v) to assess anatomical variation and determine if anatomical characters are useful for species delimitation. It was found that the genus has six centres of diversity, five of which are centres of endemism. The South African Centre is the most speciose and is also the largest centre of endemism. Kniphofia shows a strong Afromontane grassland affinity in Tropical and East Africa. In South Africa, it is found from high altitudes to coastal habitats, with the most speciose regions being Afromontane grasslands. It is thus not considered to be an Afromontane element, but rather an Afromontane associate. Five major evolutionary lineages were identified using cpDNA sequence data (trnT-L spacer), four of which are southern African. The fifth lineage is represented by material from Madagascar, East and Tropical Africa. The nuclear ITS region failed to provide resolution, as many sequences were identical. The five lineages recovered using cpDNA showed some congruence with geographic origin rather than the taxonomic arrangement based on morphology. All of the species with multiple samples were non-monophyletic. This could be due to hybridisation and/or incomplete lineage sorting. The nested clade analysis, although preliminary, did not completely agree with the phylogenetic analyses. One of the three third level nested clades appears to show fragmentation between the Cape Region, KwaZulu-Natal and northern parts of southern Africa. Furthermore, another nested clades recovered suggest a range expansion and radiation from the Drakensberg into the adjacent Drakensberg-Maputoland-Pondoland transition. Morphological species of Kniphofia exhibited substantial leaf anatomical variation and anatomical characters do not cluster samples into their morphological species. The anatomical results do not fit any geographic pattern, nor do they correspond to the lineages recovered using molecular markers or the nested clades. Leaf anatomical variation does not appear to be influenced by geographical or environmental factors. However, hybridisation may play a role but was not tested in this study. In light of the above findings it is proposed that the evolutionary and biogeographic history of Kniphofia is strongly linked to tectonic events, and Quaternary climatic cycles and vegetation changes. Tectonic events (viz. uplifts) may have resulted in vicariance events that may account for the five cpDNA lineages recovered in phylogenetic analyses, while Quaternary climatic cycles and vegetation changes may have had a more recent impact on evolution and biogeography. It is hypothesised that the ancestral area for Kniphofia was much more widespread when Afromontane grasslands were more extensive during cooler and drier glacial episodes. Kniphofia on the high mountains of Tropical and East Africa would have tracked Afromontane grasslands as they expanded their ranges in cooler periods. While during wetter and warmer interglacial periods Kniphofia would have retreated into refugia on the mountains of Tropical and East Africa, with no gene flow possible between these refugia. In South Africa, where latitude compensates for altitude, Kniphofia may have maintained a distribution that extended into the lowlands even during interglacials. A cyclic climate change hypothesis implies that populations of Kniphofia (at different phases of the climatic cycle) would have experienced periods of contractions and fragmentation followed by periods of range expansion and coalescence or secondary contact. Altitudinal shifting is proposed to be the most likely mechanism for fragmentation and range expansion, and would would possibly promoted hybridisation. Within the five lineages there is evidence for recent differentiation as the branch lengths are short, there are numerous nonmonophyletic species and numerous identical haplotypes (cpDNA and ITS) which collectively indicate a recent radiation in southern Africa. A recent radiation would also account for the taxonomic confusion and difficulty in differentiating morpho-species. These climatic events may also account for the substantial anatomical variation in southern African Kniphofia species.

Namibia, Juttadinteria and Dracophilus, the three genera belonging to the subtribe Dracophilinae Schwantes (Aizoaceae: Ruschioideae) were revised. Macro-morphology, leaf anatomy and micromorphology of leaf epidermides, pollen, tapetal orbicules and seed were studied in order to test taxon limits, to determine relationships between taxa, and to improve knowledge of their characteristics as well as the taxonomy of the subtribe. The investigation was based on herbarium specimens, field observations and cultivated, living plants. Phenetic cluster analyses were used to confirm species while intergeneric and interspecific relationships of the taxa so indicated were later tested by means of a phylogenetic analysis. The existence of the three genera was provisionally upheld by this study although phylogenetic analysis showed Namibia nested as a strongly supported monophyletic group within a poorly supported luttadinteria. Further work is needed to clarify whether Namibia should be sunk into Juttadinteria. The latest treatments of Juttadinteria and Dracophilus by Hartmann (2001) were supprted. However, in contrast to her latest treatment of Namibia, N. pomonae was sunk into N. cinerea and N. ponderosa was reinstated and typified. Juttadinteria was found to be a poorly resolved genus with many intergrading and overlapping characters, possible due to recent speciation. Possible subspecific groups within J. deserticola and J. simpsonii were indicated by the phenetic study but further work is needed before any formal infraspecific taxonomic rank can be assigned to them. Detailed descriptions of the nine elucidated species and the three genera as well as new keys for their identification are provided in order to facilitate further work in this group. Distribution maps are provided for the genera and species, and the subtribe. Variation of character states within the subtribe, distribution area, ecology and biology are discussed.

No description available.

Presented in this thesis is the mitochondrial DNA (mtDNA) cytochrome b gene analysis of the phylogenetic relationships within the Apalis thoracica complex (600bp) as well as among selected African Bradypterus species (603bp). Within A. thoracica 28 individuals from 20 subspecies were analysed. There was only molecular support for 13 historically isolated clades as opposed to the 21 subspecies recognized based on morphology. Among these molecularly defmed clades were clades lynesi, juscigularis and flavigularis, all three of which are of conservation concern and were previously treated as species by some based on their distinct morphology. Molecular clock dating estimated the clades to be of Pliocene age, whereas genetic differentiation within clades was of Plio-Pleistocene to Pleistocene age. This result is consistent with that of other African montane birds. Under the phylogenetic species concept all 11 clades could be recognised as species although a multifaceted approach to species recognition which will include vocalisation data is suggested. Contrary to expectation, the isolated East African clades did not exhibit more variation than the continuously distributed clades within southern Africa. In fact, significant phylogeographic breaks were identified within South Africa that need further investigation. For the African Bradypterus, 13 individuals from six of the 10 African species were analysed. These species were not monophyletic. Based on sequence divergence B. victorini was as different from the other members of the genus as it was from the out groups. In addition its song is very distinct and both males and females sing. Therefore, based on the molecular results presented in this thesis as well as vocalisation data and, it is proposed that B. victorini is not a Bradypterus. This result is particularly significant in light of the growing evidence that the Cape region acted as a repository for ancient animal taxa and holds implications for the conservation status of the region. The molecular data supported the classification of the taxa based on habitat and song but in addition clarified the placement of B. victorini and B. sylvaticus. The basal position of the latter among the remaining members of the genus indicates that Bradypterus is primarily a forest taxon that radiated into other habitats. It must however be kept in mind that the current dataset is based on six of the 10 African Bradypterus and none of the Asian species. The possibility of hybridisation between B. sylvaticus and B. barratti was raised and needs to be tested through additional sampling. / Dissertation (MSc (Genetics))--University of Pretoria, 2006. / Genetics / unrestricted

Thesis (MSc)--Stellenbosch University, 2003. / 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). / AFRIKAANSE OPSOMMING: Die filogenetiese verwantskappe en taksonomiese klassifikasie van Suid Afrikaanse Oxalis L. spesies is nog baie onduidelik, beide binne die gebied en ten opsigte van die presiese plasing binne die genus as 'n geheel. Vorige werk, uitsluitlik gebaseer op morfologiese en palinologiese kenmerke, was tot dusver nog net gedeeltelik suksesvol in die identifikasie van natuurlike groepe binne die inheemse taksa van die gebied. Onlangse studies op 'n paar inheemse spesies het die nut van die plastied trnL-trnF nie-koderende DNA area bevestig vir die rekonstruksie van filogenetiese verwantskappe in die genus. Hierdie studie is gerig op die taksonomiese monofilie en verwantskappe van die onnatuurlike seksie Angustatae subseksie Lineares, deur gebruik te maak van DNA basis-volgorde data. Die filogenetiese rekonstruksie van Suid Afrikaanse Oxalis spesies dui aan dat vyf van die subseksies van seksie Angustatae sensu Salter (1944) polifileties is, met sterk steun daarvoor dat drie van hulle onnatuurlik is. Die lede van subseksie Lineares is tussen drie verskillende groepe versprei; twee van dié groepe het sterk ondersteuning. Nie een van die drie groepe bestaan uitsluitlik uit spesies van subseksie Lineares nie. So ook is vier van die sewe groepe van verwante spesies binne subseksie Lineares sensu Salter (1944) polifileties. Stuifmeel data volgens Dreyer (1996) ondersteun die groepe wat deur die DNA volgordes uitgewys is, terwyl baie min morfologiese kenmerke gebruik kan word as potensiële sinapomorfe/kenmerke. Die filogenetiese rekonstruksie ondersteun dus die palinologiese data van die subseksie, en dui op die dringende behoefte aan 'n hersiening van die huidige morfologiese klassifikasie van Salter (1944).