3. Electronic Theses and Dissertations (ETDs) - All submissions
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Item Areas of neo- and palaeo-endemism in southern Africa revealed by phylogenetic measures of biodiversity in Bradypodion and Helichrysum(2017) Mahove, MichelleThe threats imposed on biodiversity by anthropogenic factors and climate change could cause major biodiversity loss that will have major detrimental effects on the livelihoods of humans and ecosystems. With time and resource constraints plaguing the conservation field it is of utmost importance that biodiversity assessments are prioritised and conducted effectively. Species richness and endemism have been used in biodiversity assessments for many years now but due to their shortcomings, phylogenetic metrics were developed. These phylogenetic metrics offer an advantage in that they include the evolutionary history and relatedness of taxa in the analysis of biodiversity, consequently providing in-depth information on the structure of a taxa and how it relates to other taxa. Phylogenetic metrics also allow the differentiation between areas of neo- and palaeoendemism, an important facet in the conservation field. Southern Africa is species diversity and endemism rich and conservation of the region is very important. Therefore, this study incorporated the use of phylogenetic metrics as well as a new metric for differentiating neo- and palaeo-endemism, CANAPE, with the aim of assessing the value of these phylogenetic metrics in identifying hotspots for biodiversity conservation in the biodiverse southern African region. The study also aimed to identify areas of neo- and palaeo-endemism in the region so as to maximise on their conservation. The widespread, everlasting daisy genus, Helichrysum (Asteraceae, Gnaphalieae) and the endemic dwarf chameleon genus, Bradypodion (Chamaeleonidae) were utilised for this study. First, phylogenetic metrics and species metrics were calculated for both genera and hotspots were inferred. The hotspots revealed by phylogenetic metrics were then assessed for overlap with the hotspots revealed by species metrics. Next, the CANAPE analysis was run so as to identify the areas of neo- and palaeo- endemism in southern Africa. A phylogenetic diversity (PD) dissimilarity analysis was then conducted to analyse the clustering of the significantly high endemic areas on the phylogenetic tree. Lastly, all the hotspots identified were assessed for representation in the protected areas of southern Africa so as to check how well they are being conserved. Phylogenetic metrics were largely congruent with the species metrics for both genera with the phylogenetic metrics revealing additional information about the taxa and its history. Bradypodion hotspots were mainly located in the Knysna area (South Africa), Walvis Bay 4 (Namibia) as well as in the Drakensberg region (South Africa) where it is likely that different niches have led to the proliferation of this genus. The results showed more Helichrysum hotspots distributed throughout the region with important areas being Sekhukhuneland, Wolkberg region, Drakensberg region, and the Maputaland-Pondoland centre of diversity in South Africa, as well as southern Namibia. Some of the phylogenetic metrics did not reveal any useful information for Bradypodion, possibly due to the small genus size. However, using the large Helichrysum genus revealed more information about the hotspots of phylogenetic diversity and endemism in southern Africa. Protection of the hotspots of neo- and palaeo-endemism still requires attention since some of the major hotspots are not located in protected areas. Such areas where conservation is still lacking were identified by the study. Plans to include the hotspots not covered by protected areas need to be prioritised to avoid the loss of speciation hubs, valuable species, and the rich evolutionary history contained within them. It can be concluded that phylogenetic metrics do reveal additional information that is important to conservation but care must be taken when making conclusions based on taxa of different sizes. Keywords: Bradypodion, CANAPE, Helichrysum, neo- and palaeo-endemism, phylogenetic metrics, southern AfricaItem Germanic and its network: representing the Germanic languages using median-joining phylogenetic networking.(2016) Hall, Andrew Peter FidleirThe two aims of this study are, first, to use lexical items to generate networks which represent relationships between various members of the Germanic language family, and second, to examine the effects of different lexical coding strategies on the placement of language nodes in these networks. This is done using old and modern Germanic languages, as well as items from reconstructed Proto-Germanic. The data was coded using amino acid codes. The median-joining phylogenetic networking program Network has been used to process the data and to generate a series of networks under various conditions. Two semantic conditions were used, a strict and a lax, and three strategies were employed to handle missing data. The generated networks were then compared with each other and also with recognised classifications of the Germanic languages. The results indicated a general three-way division in the family, although there was variation at lower levels of classification. The results also indicated the degree to which choice of lexical item and coding strategy could influence results. The study shows that more research into the utility of such quantitative methods in linguistics is required.Item A neuroanatomical evaluation of cholinergic,catecholaminergic, serotonergic and orexinergic neural systems in mammals pertaining to the phylogenetic affinities of the Chiroptera(2015) Calvey, TanyaOne of the few remaining mysteries in mammalian phylogeny is the issue of Chiropteran phylogeny. In order to further investigate the diphyletic hypothesis that states that Megachiroptera evolved from primate-like gliders and that Microchiroptera evolved from insectivores, the cholinergic, catecholaminergic, serotonergic and orexinergic systems were analyzed in, not only five insectivores (Crocidura cyanea, Crocidura olivieri, Sylvisorex ollula, Paraechinus aethiopicus and Atelerix frontalis) and three prosimian primates (Galagoides demidoff, Perodicticus potto and Lemur catta), but in species from other orders of interest including the Afrotheria (Potamogale velox, Amblysomus hottentotus and Petrodromus tetradactylus), Lagomorpha (Lepus capensis) and Scandentia (Tupaia belangeri). Brains of the mammals were coronally sectioned and immunohistochemically stained with antibodies against cholineacetyltransferase, tyrosine hydroxylase, serotonin and orexin-A. The presence or absence of 93 nuclei within these neuromodulatory systems was entered into modern cladistics software for analysis of the 13 studied species, as well as an additional 40 previously studied mammals. The majority of nuclei revealed in the current study were similar among the species investigated and to mammals generally, but certain differences in the nuclear complement highlighted potential phylogenetic interrelationships. The Afrotherian, A. hottentotus, presented unusual cholinergic interneurons in the cerebral cortex, hippocampus, olfactory bulb and amygdala, and exhibited an unusual foreshortening of the brain, such that a major mesencephalic flexure in the brainstem was evident. The Afrotherian, P. tetradactylus, lacked the catecholaminergic A15d nucleus as in a previously studied member of Macroscelididae. The three Insectivoran shrews lacked the cholinergic parabigeminal and Edinger-Westphal nuclei, had a mediodorsal arch of the cholinergic laterodorsal tegmental nucleus, lacked the catecholaminergic A4 and A15d nuclei and presented an incipient ventral division of the substantia nigra which is identical to previously studied Microchiroptera. All three prosimians presented a central compact division of catecholaminergic locus coeruleus (A6c) surrounded by a shell of less densely packed (A6d) tyrosine hydroxylase immunopositive neurons. This combination of compact and diffuse divisions of the locus coeruleus complex is only found in primates and Megachiropterans of all the mammalian species studied to date. T. belangeri of the Scandentia contained ChAT+ neurons within the nucleus of the trapezoid body as well as the superior olivary nuclear complex, which has not been described in any mammal studied to date. L. capensis of the Lagomorpha presented vi the rodent specific rostral dorsal midline medullary nucleus (C3), while T. belangeri was lacking both the ventral and dorsal divisions of the anterior hypothalamic group (A15v and A15d), and both species were lacking the primate/Megachiropteran specific compact portion of the locus coeruleus. Our neuroanatomical analysis suggests a phylogenetic relationship between the Soricidae (shrews) and the Microchiropterans, supports the phylogenetic grouping of primates with Megachiropterans, confirms previous molecular evidence of the relationship between lagomorphs and rodents within the super-order Glires, and suggests that primates are phylogenetically closer to Megachiroptera than to any members of the Euarchontoglires. The cladistic analysis confirmed the neuroanatomical analysis with the most parsimonious tree placing Megachiroptera into the Euarchontoglires as a sister group to primates and the Microchiroptera next to Soricidae within the Laurasiatheria.Item The behaviour of two sub-species of the striped mouse Rhabdomys: the role of phylogeny and the environment(2011-09-14) Mackay, Megan KirstenThe role of phylogeny and environmental influences on behaviour were investigated in two sub-species of Rhabdomys dilectus: R. d. chakae and R. d. dilectus. I compared populations of the two sub-species that occur about 70 km apart in superficially similar grasslands, south of Johannesburg (Walkers Fruit Farms) and at Irene in Gauteng Province, South Africa. The vegetation characteristics of the localities were assessed by measuring aerial cover, cover density, amount of dead material, and the maximum and minimum plant height. I studied the maintenance (non-social) and social behaviour of the sub-species in captivity. Three maintenance behaviours were studied: diel activity in an open arena, activity in an enclosed maze and in a modified plus maze. Social behaviour was studied by investigating the stress response of juvenile males after removal from their family groups and being placed in a plus maze, and the tolerance of unfamiliar same-sex consub-specifics in staged dyadic encounters. My results indicate that there were differences in the vegetation at the localities, most notably in the level of cover, which was greater at Irene (R. d. dilectus) than at Walkers Fruit Farms (R. d. chakae). Both sub-species displayed similar activity profiles (diurnal and crepuscular) and similar levels of activity in an enclosed maze. However, R. d. dilectus showed high levels of anxiety in an open arena and in a plus maze. The sub-species showed similar social behaviours: males of both sub-species that were removed from their family groups at the onset of weaning showed a lower stress response compared to the social sister species R. pumilio. Social interactions of same-sex intra-sub-specifics were mostly similar between the sub-species but there were slight discrepancies in behaviour associated with mating. Surprisingly, there were higher levels of amicability in all dyads than predicted by the solitary lifestyle of the two sub-species in nature. Behavioural differences (anxiety response) may be due to divergence in allopatry because of differences in vegetation characteristics. The similarities in activity profile and social behaviours could be explained by phylogenetic inertia or by similar selection pressures in similar environments.