The Core Cape Subregion (CCR) is made up of a mosaic of highly weathered and nutrient leached soil substrates in the Western Cape. Plant available phosphorus (P) in these soils is very low, generally ranging from 0.4-3.7 µg P g-1 soil and as a result plants have evolved a number of traits to enhance P-acquisition, such as increased root surface area (SA) and specific root length (SRL), cluster root and root hair proliferation and exudation of organic acids and acid phosphatases (APase) from the roots. Crop yield is limited worldwide due to the unavailability of P and P-fertilization is showing limited success due to soil retention. Sustainable management of this would include exploiting plants with natural adaptations for enhanced P acquisition and utilization. The aim of this study was to discover whether cluster root forming species are more efficient at P acquisition than non-cluster root species. This was achieved by focusing on two objectives: (1) to characterize root traits for increased P acquisition in different soils of the CCR and (2) comparing P-uptake and utilization efficiencies of cluster root species to non-cluster root species under glasshouse and natural conditions. Plants from Fabaceae, Polygalaceae, Proteaceae, Cyperaceae, and Juncaceae were grown in two different glasshouse experiments and observed in a field study.

The common hippopotamus (Hippopotamus amphibius) is endemic to Africa but threatened by range restriction, exploitation and competition with humans and domestic livestock for access to critical resources such as fresh water and grazing. Collectively these impacts have resulted in population declines throughout most of their range with the consequence that hippos are classified as Vulnerable on the IUCN Red list. Despite these threats to their persistence and their important ecological role as ecosystem engineers there have been surprisingly few studies concerning factors that influence their current distribution and habitat use. Such research is important for developing effective conservation and management plans to improve the protection of vulnerable and ecologically important species such as hippo. South Africa is home to one of a few growing hippo populations and one of the last persisting in an estuarine habitat. The St Lucia Estuary, one of three Ramsar Wetlands of International Importance located in the iSimangaliso Wetland Park (itself a UNESCO World Heritage site), in northern KwaZulu-Natal is not only the largest estuarine system in Africa, but is also home to one of South Africa's largest hippo populations. In this study I explore aspects of the spatial and behavioural ecology of hippo within the St Lucia Estuary. More specifically, I investigate select abiotic and biotic predictors of hippo presence and the frequency with which they return to their diurnal lie-up sites. I used binary logistic regression models to evaluate the effects of the selected habitat features on hippo occurrence at two spatial scales (broad and fine). I used a negative binomial with log-link model to evaluate the effects of the selected habitat features on the frequency of use of sites (hippo persistence) in the fine-scale study. In addition, I employed both instantaneous scan sampling and continuous sampling methods in an attempt to determine the diurnal activity budgets and social interactions of a single group near the mouth of the St Lucia Estuary. I used non-parametric tests to evaluate differences in behaviour with daytime and across sampling days with a view to an improved understanding of how the environment influences the behaviour of hippo in an environment subject to ongoing human modification.

The dicynodonts are an extinct group of herbivorous non-mammalian synapsids that were fairly abundant in Gondwanan deposits of the middle Permian to the Early Triassic periods. The extinct genus Endothiodon was first described by Sir Richard Owen in 1876, and is well known from the late Permian deposits of the Karoo Basin of South Africa. It is characterized by rows of internal teeth on the premaxilla and dentary arranged in replacement waves called Zahnreihen; longitudinal ridges running from the premaxilla to the pineal crest; and a prominent pineal boss with a pineal foramen. Endothiodon is well-represented by cranial and postcranial material in the Karoo vertebrate collections at various museums in South Africa. The repeated taxonomic revision of this genus over the years has led to much confusion about what constitutes the type species, E. bathystoma. Recently, an almost complete skeleton of Endothiodon (SAM-PK-K011271) was recovered from the uppermost Pristerognathus Assemblage Zone of the Karoo Supergroup. The fossil comprises the skull and most of its postcranial elements preserved in articulation. The current study provides a comprehensive description of the anatomy of this specimen, which permitted its identification as E. bathystoma. Furthermore, by comparison with other South African Endothiodon specimens this study determined that this specimen is the second largest E. bathystoma specimen known to date. The well-preserved skull and postcranial skeleton of SAM-PK-K011271 makes it an ideal reference specimen for E. bathystoma and has permitted a good assessment of its overall anatomy. The findings of this study provide a perfect stepping-stone for future studies to further address E. bathystoma’s skeletal reconstruction and biomechanical functions, as well as other aspects of the palaeobiology of this animal.

Insects, including wild bees (Hymenoptera: Anthophila) are exceptional model organisms to assess the effect of climate variation on species richness along altitudinal gradients. Climate variables and weather conditions are of extreme importance for insects particularly since their capacity of body temperature regulation is determined by the ambient temperature. Additionally, bee diversity has proven to be strongly related to the availability of host plants, determinant factors for their presence or absence and both of which are limited at higher altitudes. Therefore, the study of wild bee diversity at various altitudes in the tropics could provide information on possible responses of bee species and communities to climate variations, important to estimate effects of climate change on an important ecosystem service such as pollination. Bees being ecologically important insects with close links to plants, high richness and abundance are well-suited as terrestrial habitat bioindicators. The group is sensitive to environmental disturbances relies upon local plant communities and comprises an assemblage of species with varying social structure, nesting guilds and other life history traits. Additionally, bees are likely more susceptible to negative effects of small effective population size. The life history traits determine the individual and community response to environmental changes. Records from the literature revealed a collector and seasonal bias, with greater effort applied around big cities or specific collecting locations and mainly in the wet season. A preliminary checklist of bees of Angola was created and comprises 209 bee species from 47 genera and five families, but a major proportion of the country's area remains to be surveyed. A national inventory of Angolan bees is proposed, making use of standardized methods and sampling either one quarter degree cell or half degree cells, ideally in both dry and rainy seasons. Wild bee communities were sampled along an altitudinal gradient (760-1651 m.a.s.l) in the biodiversity rich and critically endangered Angolan escarpment. Pan traps, malaise traps and sweep netting were used at twelve sampling points, with an average of 70 m difference in altitude between points. Sweep netting proved to be the most efficient technique. Overall, 845 individuals were collected, representing 51 identified species, 34 genera and five bee families. Contrary to the trends observed in other studies in the tropics, a consistent increase in bee diversity (carried out at genera level) with increasing altitude, from the lower altitude (H'=2,14) to the higher altitude of the gradient (H'=2,26) was found. In addition, community structure differed along the gradient, with distinctive communities in low elevation sites being dominated by Braunsapis, Ceratina, Hypotrigona and Anthidiellum, and high elevation sites the distinctive communities were dominated by Amegilla, Macrogalea, Patellapis and Xylocopa. This result might be consistent with findings from studies of other taxa that attribute to the Angolan escarpment an importance as a centre of endemism and speciation. The results from this study are possibly explained by a combination of factors where the exceptional geomorphology and landscape shape the (direct) influence of environmental variables such as temperature and precipitation on the vegetation communities along the gradient therefore (indirectly) affecting bee community assemblages, particularly for the more specialized bee genera and species. Limited research has been done on the variation of bee body size along altitudinal gradients, but the few studies that have been carried out indicate that future changes (warming) in climatic conditions will most probably alter bees body size (by reduction), consequently affecting their thermoregulatory capacity and, at a larger scale, the overall patterns of community assembly. Along the tropical altitudinal gradient of this study, bee body size was found to increase with altitude by 58% (mean length at lower altitude = 5.06mm against mean = 7.99mm at higher altitude elevation sites) at the community level but also at the intra-specific level, with Macrogalea candida increasing 4% in size between the lower altitude and summit of the transect (mean length at lower altitude = 8.76mm against mean = 9.12mm at higher altitude elevation sites), suggesting that the fairly small temperature gradient along the transect was sufficient to select for body size – either directly, but more likely through multiple avenues, including indirect effects such as changes in rainfall, plant community composition and plant phenology. This result constitutes, to my best knowledge, the first demonstration of Bergmann's rule applicability at different levels of biotic organization of bee communities in the tropical region. Effective conservation planning is highly dependent on robust, spatially explicit biodiversity data. The generation of comprehensive insect profiles through long term monitoring studies at the national level can identify areas with high species turnover and endemism – patterns that could be missed if only vertebrate data were considered. In under-developed countries like Angola, where a poorly documented but highly rich biodiversity is severely threatened by unregulated land use, and research is hampered by financial constraints and lack of human resources, the combined use of indicator taxa for both terrestrial (bees) and freshwater (Odonata) environments might be a reasonable surrogate for total biodiversity status assessments. The results from this study highlight the need for long term monitoring to efficiently assess bee diversity, especially in critically endangered landscapes where anthropogenic pressures are high.

Includes abstract. / Includes bibliographical references. / Yellowtail, Seriola lalandi, is an important line-caught fish in South African waters, yet little information is available on their life-history. This study aims to add information on the diet and feeding habits, reproductive biology and the age and growth of yellowtail in South Africa. The diet of 62 yellowtail caught in the Western Cape of South Africa between 2011 and 2012 was investigated. Fish sampled by line and speargun ranged from 488 to 916 mm fork length (FL). Prey items were removed from stomachs, sorted, counted and weighed in order to calculate the percentage number (% N), percentage weight (% W), frequency of occurrence (% F) and index of relative importance (% IRI). Of the 62 stomachs examined 11 (17.7 %) were empty, 16 (26.0 %) contained only unidentifiable remains and 47 (82.5 %) contained identifiable remains. Prey items covered 18 species belonging to five classes: bony fishes, crustaceans, cephalopods, polychaetes and bivalves. Small pelagic fish were the dominant prey type, followed by crustaceans. The remaining taxa were of negligible importance. Some dietary differences were observed between sample areas. Most notable was the increased importance of crustaceans at Dassen Island on the West Coast compared to the sites at Robben Island, False Bay and Struisbaai. The reproductive characteristics of yellowtail were documented from fish collected from 1974 to 2012. Samples were collected from Cape Infanta on the South Coast to Lamberts Bay on the West Coast of South Africa. Histological validation of macroscopic staging criteria revealed that active and developing ovaries are commonly staged incorrectly. A protracted spawning season from November to February with peak spawning in December and January was deduced from GSI values. No hydrated eggs were observed. Females matured at 550 mm FL (95 % CI = 532 - 570 mm) and males matured at 585 mm FL (95 % CI = 555 - 619 mm). The age and growth characteristics of yellowtail in South African waters were determined from readings of whole sagittal otoliths collected from 1974 to 2012. Whole otoliths were considerably easier to read than sectioned otoliths. A total of 524 whole otoliths were taken from fish ranging from 430 to 1080 mm FL, of which 141 (27 %) were discarded and 384 (73%) were readable. Agreement between all three readers was 13 % (n = 50) and between any two was 71 % (n = 274). Maximum ages for male and female yellowtail were 7 and 8 years respectively. Age at 50 % maturity (A50) for males it was 2.3 years while females matured (A50) at 3.6 years. Von Bertalanffy growth parameters did not differ between males and females (P > 0.05). A statistical penalty was used to keep the estimated growth parameters within biological limits and produced a von Bertalanffy growth equation with an L∞ and K of1064 mm and 0.17 y-1 respectively. The growth performance index (φ) of yellowtail in South African waters was found to be 3.51. This is high for the family Carangidae but on par with other species in the genus Seriola. The life history characteristics for yellowtail in South African waters closely resemble those of other yellowtail populations. The diet of yellowtail in South African waters represents that of a robust generalist feeder that is not reliant on specific prey for its survival. The age, growth and reproductive characteristics of yellowtail in South African waters indicate that they are a fast growing and relatively early maturing species. These life-history characteristics indicate that the stock is resilient in relation to other line-fish species, but the large proportion (41%) of fish caught below the 50 % size at maturity suggests that a revision of the minimum size limit should be considered.

For several decades Vachellia and Senegalia have been assumed to be ecological equivalents in African savannas. Their supposedly close evolutionary relationship has, however, been totally revised in light of recent molecular phylogenetic data. These data highlight the deep divergence (± 30 Ma) between these genera and also their independent transitions into African savannas. Distant divergence and independent transitions into savannas between Vachellia and Senegalia suggest their possible ecological niche divergence, which could explain the observed differences in invasiveness between them. This thesis provides the first ecophylogenetic study to assess the level of ecological niche divergence between these economically, socioeconomically and ecologically important tree genera in Africa. I address this question by first determining the scale(s) of coexistence between Vachellia and Senegalia and determine their phylogenetic community structure at both the landscape-regional scale and the plot-scale. I then conduct a large glasshouse experiment using seven species from each genus to determine conserved functional differences between them during seedling establishment in the presence, and also the absence, of grass competition. While I find evidence of some Grinnellian niche differentiation between Vachellia and Senegalia at the landscape-regional scale, their greater-than-expected co-occurrence in plots suggests they generally partition an Eltonian niche in savannas. Glasshouse trait data also reveal that Vachellia has a conserved strategy for rapid vertical growth when free from grass competition and Senegalia has a conserved root tissue density response to grass competition. I argue that the rapid growth (bolting) strategy of Vachellia in the absence of grass competition provides a functional explanation for why this genus is observed to be relatively more invasive in grassy ecosystems. I also argue that the root tissue density response of Senegalia enables stable coexistence at the plot scale with Vachellia as it increases competitive ability among grasses leaving establishment less tied to times of low grass biomass. I conclude that this study provides overwhelming support for ecological niche divergence between Vachellia and Senegalia and that this divergence may underpin their observed differences in invasiveness. That the coexistence of these genera is largely attributable to Eltonian niche partitioning also provides fresh support for the contention that tree-tree competition structures tree communities in African savannas. Finally, niche divergence suggests that, when promoting diversity and managing invasion, Vachellia and Senegalia species will require different management practices.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 143-163). / Three-dimensional in vitro tissue and organ cultures have immense promise as models of human pathophysiology and stand to make a significant impact on the process of drug discovery and development. Many existing model systems do not capture the relevant complexity of the native tissue environment, relying on poorly characterized natural extracellular matrices (ECMs) for growth and development. These models are notably limited by the lack of vasculature, a key functional component of most human tissues, enabling oxygen and nutrient exchange, as well as facilitating paracrine signaling with surrounding epithelial cells. Fully-defined and tunable synthetic ECMs that support the generation of vascular network structures in dense tissue environments represent a path towards overcoming the limitations of existing model systems. / This thesis focuses on the development and characterization of polymeric biomaterials that can be used to enhance in vitro tissue models through engineering the cell-material interface to guide a particular biological response. A major application focus of this research is to engineer biomaterial tools that would enable vascularization of dense epithelial tissue in vitro. We developed and characterized a poly(ethylene glycol)-based microbead angiogenesis scaffold with tunable physical and biochemical properties, identifying a critical ligand concentration regime on the microbead surface that promotes integrin-mediated endothelial cell attachment and invasion into both a synthetic ECM as well as a tissue aggregate of hepatocarcinoma cells. / Furthermore, we investigated a novel hybrid PEG-polypeptide polymer, poly([gamma]-propargyl- L-glutamate) (PPLG) as a hydrogel substrate that can enhance endothelial cell attachment and spreading through modulation of the macromer structure and hydrophobicity properties. This work demonstrates how rational biomaterial design through chemical and structural modifications to polymer scaffolds can control cell fate within an in vitro tissue culture system. / by Marianna Sofman. / Ph. D. / Ph.D. Massachusetts Institute of Technology, Department of Biological Engineering

Parasites are a vital component of ecosystems. However, their contribution to the functioning and structuring of ecosystems has historically been overlooked worldwide. In South Africa, marine ichthyoparasitology has a long history but research has largely been confined to taxonomic studies and the literature pertaining to marine ichthyoparasites is highly fragmented. This situation makes it difficult to gauge advances in marine parasitology, identify knowledge gaps and hampers our understanding of their ecological roles in the marine environments of Southern Africa as well as their use as tools in fisheries science. This thesis aims to explore the diversity of metazoan marine ichthyoparasites reported from Southern African waters and to examine their inter- and intraspecific distribution in marine fishes. A review of two centuries of parasitological literature, 1818 to 2017, revealed that 378 marine ichthyoparasites have been recorded off South Africa and included taxa from six phyla: Acanthocephala (12), Annelida (6), Arthropoda (210), Cnidaria (11), Nematoda (6) and Platyhelminthes (133). The parasites formed 723 unique host-parasite pairs with 269 host taxa spread across the classes Actinopterygii (186), Elasmobranchii (80), Holocephalii (2) and Myxini (1). Host species with the most diverse parasite assemblages were species of commercial significance, namely Thyrsites atun (20) followed by Merluccius capensis (17). The dominance of arthropods and platyhelminthes, which together accounted for 90.7% of the parasites found, reflects the interest and expertise of local and foreign researchers who have worked in South Africa. The parasite assemblage of selected commercially significant fish species was used to assess the degree of interspecific similarity in parasite community structure and identify the drivers of ichthyoparasite community assembly in the Southern Benguela. The examination of 554 specimens comprising six fish species (Brama brama, Chelon richardsonii, Merluccius capensis, Merluccius paradoxus, Sardinops sagax and Thyrsites atun) caught off the South African west coast revealed that they hosted 41 metazoan parasite taxa. These included 10 new host records and five new geographic records. Thyrsites atun and C. richardsonii had the most speciose component communities being infected by 17 and 14 taxa respectively. Multivariate analyses revealed that host habitat and identity in conjunction with the host specificity of ectoparasites influenced the community structure of ectoparasitic assemblages. Larval endoparasite community structure, on the other hand, differed between inshore and offshore habitats. Within the offshore habitat, further variation in endoparasite communities were driven by the host species‘ position in the food web, its trophic ecology and its vulnerability to potential final hosts of larval parasite taxa. A survey of the metazoan parasites of snoek (Thyrsites atun) caught in the Southern Benguela (n = 262) and the Northern Benguela (n = 87) revealed 18 taxa comprising 12 new geographic records for the Northern Benguela. A generalised additive mixed model (GAMM) indicated that infracommunity richness of snoek was determined by host size. Multivariate analyses revealed an ontogenetic shift, driven by an increase in the prevalence and infection intensity of trophically transmitted taxa (Anisakis sp., Corynosoma australe, Hepatoxylon trichiuri, Molicola uncinatus), in infracommunity structure as well as in the long-lived larval parasite assemblage. A ‗Random Forest‘ analysis selected Anisakis sp. and M. uncinatus as potential biological tags for assessing the population structure of snoek in the Benguela ecosystem. GAMMs with binomial and Tweedie error distributions were used to respectively assess the prevalence and abundance of both selected taxa in relation to host traits, seasonality and region of origin. The analyses demonstrated that anisakids were more prevalent and abundant in snoek caught in the Southern Benguela while M. uncinatus were more prevalent in snoek from the Northern Benguela. The spatial differences in infection levels of both parasite taxa suggest the presence of two snoek populations in the Benguela ecosystem. The information collected, collated and presented in this thesis has enabled an assessment of the present state of marine ichthyoparasitology off Southern Africa. Although the work uncovered a diverse ichthyoparasite fauna, it also revealed a bias towards particular parasitic taxa. The study highlighted a need for wide-ranging parasite surveys not restricted to certain host or parasite taxa in order to improve our knowledge of marine ichthyoparasite diversity in South Africa. The thesis also provided the first assessment of the drivers of parasite community assembly in the Southern Benguela and demonstrated that host ecology and the characteristics of the parasites played an important role in determining their distribution and interspecific distribution. Geographic differences in snoek parasite distribution patterns which reflect ecological variations across ecosystems have also proved useful to inform fishery management.

Includes abstract. / Includes bibliographical references. / This thesis sets out to establish how extensive pastoral systems have changed and investigated the role of the key legislative and policy influences on these changes. It examined the current key drivers of pastoral mobility and analysed the different movement patterns and their spatial extent within a spatially constrained environment. This thesis also investigated the role of vegetation type and condition in the distribution of grazing pressure and further discussed the implications of using variable stocking rates in a spatially constrained pastoral system.

Includes bibliographical references. / Lowland renosterveld is a relatively fertile, shale-derived vegetation type found within the FynbosBiome of South Africa, a biome which is recognized as one of the world’s smallest, yet richest plant kingdoms. Due to the fact that renosterveld tends to be dominated by a handful of small-leaved asteraceous shrub species, it creates the illusion that it is a homogeneous habitat with low levels of alpha diversity and species turnover. This is exacerbated by the widely accepted, although not proven, hypothesis which states that current-day renosterveld is derived from a pristine C4 grassland and that the dominance of asteraceous shrubs is solely due to more than 300 years of mismanagement in the form of overgrazing. This process of degradation is believed to have started with the arrival of the European settlers who exterminated the large herds of free-roaming ungulates and replaced them with livestock (sheep and cattle), which, through their selective feeding habits and their sedentary manner of grazing, altered the system from a grassland to a shrubland. The debate over what renosterveld actually is, combined with a dearth of knowledge as to its ecological functioning, has meant that management recommendations are largely based on a combination of guess-work and inferences from studies in adjacent and similar fynbos and karoo habitats. Additionally, renosterveld has been severely transformed for agricultural development, rendering it a Critically Endangered vegetation type, with 4- 10 % of the original extent remaining.In this thesis, I focus on lowland renosterveld in the Overberg (also referred to as South Coast Renosterveld), Western Cape, South Africa. I investigate, through the use of soil carbon-isotope analyses, the grassy-shrubland vs. shrubby grassland debate and assess whether or not the theory that renosterveld is merely a degraded grassland has merit. I evaluate diversity levels at the alpha, beta and gamma scales and contrast these with comparable Mediterranean-climate vegetation types, while considering the implications for conservation planning for renosterveld in the Overberg. Through the use of a simple model, I investigate whether it is possible to predict species extinction rates at the local (patch) level. I then assess responses to grazing and fire, through a combination of controlled experiments and random surveys, in order to assess management requirements.I found that South Coast Renosterveld was more-than-likely always a grassy-shrubland, and that although data suggest slightly higher C4 inputs historically, renosterveld was never a pure C4 grassland. Alpha diversity was on a par, if not higher, than that of any other studied fynbos habitats and is comparable, if not richer, than its other Mediterranean-climate shrubland counterparts. Similarly, species turnover across habitat and landscape gradients was high, suggesting that multiple renosterveld as a functioning ecological entity at the landscape level.