Includes bibliographical references. / The Diep River estuary is a small, urban estuary situated in the suburbs of Cape Town and has been subjected to long-term modifications and abuse that far exceeds that of most other estuaries around South Africa. Activities in the Diep River catchment, together with the intensive urban development in the areas adjacent to the estuary, have resulted in massive changes in biodiversity, altered flow and salinity regimes; causing a marked deterioration in water quality and a frightening increase in non-indigenous species introductions. Several studies have been undertaken at the Diep River estuary, however, they are out-dated and many changes have occurred within the last few decades. The aim of this study was to provide an up-to-date list of the fauna residing within the Diep River estuary, as well as to provide a synthesis of all the major physical, hydrological and faunistic changes that have occurred within and around the estuary, dating back to the late 1800s, whereas faunistic changes are described using information provided by several earlier surveys dating back to the early 1950s. Infauna, epifauna and salinity were taken at designated stations along Milnerton Lagoon. Prawn (Callichirus kraussi) counts were also made in order to determine current abundance and distribution. Results showed a substantial decline in sand prawn abundance with the estimated standing stock calculated at just over 12 million. Fauna collected were generally poor in abundance and were mainly limited to euryhaline, detritus feeders. Earlier surveys conducted in the 1950s recorded at least 49 infauna and epifauna species residing within Milnerton Lagoon, whereas in 1974, only 23 species were found. Similarly, 24 species were recorded in this study. The European shore hopper (Orchestiagammarella) was recorded as a new introduction within the system. Only five fish species were recorded in the summer period, including the highly invasive mosquito fish (Gambusiaaffinis), which was found in relatively high abundance within the lagoon. A regular monitoring of the infauna and epifauna populations for this system needs to be established, in order to obtain a clear picture of the faunistic distribution and changes occurring within this highly dynamic environment. Additionally, serious management protocols need to be established in order to prevent the further degradation of this important system.

Although scallops have a high economic value, they have yet to be commercially harvested or farmed in South Africa. Of the 29 Pectinid species recorded on the southern African coastline, Pecten sulcicostatus is the only species considered suitable for aquaculture, due to its large size. An investigation of the suitability of P. sulcicostatus for farming in South Africa forms the basis of this study. The successful cultivation of P. sulcicostatus will depend on successful rearing from fertilized egg to market size, and achieving a growth rate comparable to that of other commercial scallop species. This study aimed to examine the reproductive life cycle, in order to establish whether this species can be artificially conditioned to produce ripe gametes throughout the year and to investigate the various stages of cultivation, in order to determine whether this species is viable for farming. This thesis therefore describes the reproductive cycle of P. sulcicostatus and also reports on the first assessment of broodstock conditioning, larval rearing and the grow-out of spat. The reproductive study was undertaken by monthly collection of scallops in their natural habitat in False Bay from August 2004 - October 2005 and again from August 2010 - August 2011. The reproductive cycle was assessed by means of both gonadosomatic index (GSI) and qualitative and quantitative histological investigation. Environmental parameters were also monitored to determine any linkage to the reproductive cycle. The reproductive cycle was seasonal, with a peak spawning period in winter. A resting period appeared absent, as individuals started producing new gametes immediately after spawning, indicating a possible lack of synchronicity.

The southern African echiuran fauna currently comprises two families, four genera and eighteen species. The taxonomic positions of three other species, one of Ochetostoma and two of Thalassema, remain to be resolved. Of the recorded species, three are new to science and a further five are new records for the southern African region. This survey reveals that there are ten species of Ochetostoma, four of Thalassema and three of Anelassorhynchus. The family Echiuridae contains a single genus, Echiurus and in southern Africa, E. antarcticus is the only species recorded to date. Full descriptions of the new species and those formerly inadequately described are given. The diagnoses of some others are modified and, where necessary, additional notes added. Keys for the identification of families, genera and species are provided and the taxonomic characters are evaluated and discussed. The zoogeographic distribution of the southern African species is mapped and an attempt has been made to analyse the recorded species on the basis of faunistic provinces. The phylogenetic position of the Echiura in the system of the animal kingdom is discussed. The lack of any form of segmentation of the mesodermal bands during embryonic developnent seems to justify their status as a separate phylum. The biomechanics of burrowing, locomotion and trunk irrigatory movements of Ochetostoma caudex are described and compared with the activities of some other animals with unsegmented coelomic cavities. Pressure changes within the coelom have been measured with the use of electronic recording techniques and the results interpreted in relation to direct visual observation. The anatomy of the reproductive system and the process of gametogenesis in O. caudex have been investigated with light and electron microscopes. Some observations on aspects of breeding behaviour and spawning are also included.

Prions (Pachyptila spp.) are one of the most abundant seabird groups of the Southern Ocean but their taxonomy, at-sea distribution and foraging ecology are poorly known. There has been considerable confusion surrounding the taxonomy of prions and their identification at sea is problematic. Recent studies have confirmed the presence of two very similar prion species breeding sympatrically, approximately three months apart, on Gough Island: Pachyptila vittata and P. macgillivrayi. This discovery raised several questions about the ecological segregation of these species. My thesis compares the breeding distribution, at-sea movements, phenology, foraging ecology and trophic segregation of the two species at Gough Island, and compares Gough birds with the P. vittata from Tristan da Cunha. In 2000/01 it was estimated that 1.5–2.0 million pairs of prions bred on Gough Island, suggesting that this site supports the largest populations of both species in the world. However, the contribution of each species to this total as well as spatial and temporal segregation of the two species required further investigation. To investigate the breeding distribution and relative species proportions across Gough Island, 2227 prion specimens were collected opportunistically over several years at various sites. Most birds were caught at night or found dead, thus only provide an inference of breeding distribution. However, observations of incubating birds at several sites indicate that the data are representative of nesting distributions. At most sites there was evidence for consistent dominance of one or other species, although this need not mean local allopatry; a few P. vittata breed in Prion Cave, where P. macgillivrayi is by far the most abundant species. A few sites had both species in similar proportions, but these tended to be sites with relatively few birds and/or represent areas where the two species’ ranges abut. Weighting each site equally suggested a roughly equal ratio of P. vittata/P. macgillivrayi, but there was little coverage of the northern and eastern glens, where P. vittata appears to predominate. The habitat area occupied by P. macgillivrayi comprises ~40% of Gough Island, suggesting they comprise ~40% of the prion population if the density of breeding birds is roughly similar for both species. Based on these proportions and the previous population estimate, some 600 000 to 1 000 000 P. macgillivrayi and 750 000 to 1 200 000 P. vittata are estimated to breed on Gough Island Additional investigation is required to elucidate the spatial segregation of the two species at a finer scale. Additional detailed categorizing of habitat types is needed to determine the fine-scale drivers for their spatial segregation. The prions’ phenology, foraging ecology and trophic segregation was examined through geolocation technology, salt-water immersion sensors (recording time on the water), stable isotope analyses as well as a comparison of bill morphology. Breeding adults of both species were tagged with geolocators/immersion sensors on Gough Island and breeding adults of P. vittata were tagged at Tristan da Cunha. During their respective breeding seasons P. vittata largely remained within 1500 km to the north-east of the colony and P. macgillivrayi occupied waters within 1000 km to the south of the colony. At Gough Island, P. vittata departed and returned to the colony on average 91±9 days earlier than P. macgillivrayi. The length of the non-breeding period did not differ between species and all tracked individuals except one P. vittata engaged in a pre-laying exodus lasting 13-49 days. The P. vittata population from Tristan da Cunha departed, moulted and returned 15-17 days later than their counterparts from Gough Island. After breeding, both species showed a well-defined outward migration, with all moving west until the start of moult, except one P. vittata individual that moved east. Moulting was inferred from a marked reduction in the time spent in flight, which occurred shortly after arrival on the non-breeding grounds by both species (i.e. November– February for P. vittata and February–June for P. macgillivrayi). Moulting birds targeted specific areas with little overlap between species within the Argentine Basin. Both species briefly returned to their burrows after moulting. During the remainder of the non-breeding period both species were distributed more widely over the South Atlantic Ocean. Interspecific spatial segregation was observed for most of the tracking period, especially in core use areas. Pachyptila macgillivrayi spent more time flying, during both daylight and darkness, than P. vittata. Stable isotope signatures of prion flight feathers from tracked birds and additional samples from each population indicated that movements of tracked individuals were representative of the adult population, and were similar over years. Higher δ 15N values found in P. macgillivrayi feathers is consistent with the hypothesis that P. vittata, being the more specialist filter feeder, targeting copepods, should forage at a lower trophic level than the more generalist P. macgillivrayi. This is also consistent with the greater time in flight for P. macgillivrayi i.e. more time actively searching for food, rather than sitting on the water filtering. Across both species, bill width was positively correlated with the number of palatal lamellae with P. vittata having a wider bill containing more palatal lamellae and thus better equipped for filter feeding. Habitat analysis revealed biologically meaningful, speciesspecific preferences for distance from the breeding colony, chlorophyll-a and sea surface temperature, but not distance to seamount or for water depth. This study contributes to the growing number of studies tracking small petrels and provides information on the strategies employed by extremely similar and abundant seabirds, most notably allochrony for P. vittata and P. macgillivrayi, allowing ecological segregation as well as furthering the understanding of moult in prions. The findings of this thesis advance the knowledge of the ecology of these poorly studied species of prions.

Includes bibliographical references (p. 215-229). / The research in this thesis examines the links between benthic macroinverebrate (invertebrate) distributions and aspects of the physical habitat at different spatial and temporal scales in mountain and foothill zones of rivers in the Western Cape, South Africa. A geomorphological hierarchy was used as the spatial template for studying invertebrate distributions. The different levels of the hierarchy are: catchment, segment, zone, reach, morphological unit and hydraulic biotype. Hydraulic biotypes are visually defined flow and substratum combinations. The hierarchical levels studied in this thesis were catchment, zone, reach and hydraulic biotype.

Includes bibliographical references. / This study describes the impact of longline fishing on the seabirds breeding on the sub-Antarctic Prince Edward Islands. The development of a demersal longline fishery for Patagonian toothfish Dissostichus eleginoides close to the islands with almost complete observer coverage during the study allowed a detailed examination of the impacts of this fishery. The vast majority of seabird mortalities were adult males that were breeding at the time they were killed. White-chinned petrels Procellaria aequinoctialis were killed most frequently, but albatrosses and giant petrels were also killed when lines were set in the daytime. Birds were killed almost exclusively during their breeding season, and albatrosses were caught closer to the islands than whitechinned petrels. It is estimated that between 8 500 and 18500 birds could have been killed between 1996-2000, mostly due to high levels of Illegal Unregulated and Unreported (IUU) fishing. This is likely to have a significant impact on the breeding populations of several species of seabirds breeding on the Prince Edward Islands. A large increase in the amount of fishing gear found next to seabird nests as well as fishery-derived items in the diets of wandering albatrosses was recorded concurrent to the development of the toothfish fishery around the Prince Edward Islands. There was also an increase in the number of observed seabird entanglements in fishing gear and mortalities due to the ingestion of fishing gear.

The world-wide proliferation of dams in the last few decades has necessitated a fuller understanding of the effects of stream regulation but has also provided a setting for testing and developing basic theories of stream ecology. Two important concepts in stream ecology, the River Continuum Concept (RCC) and the Serial Discontinuity Concept (SOC), required investigation as to their applicability to entire river systems in the Southern Hemisphere. The RCC hypothesises that biological communities are structured in a predictable fashion from the source to the mouth of a river in relation to physical environmental gradients along the stream continuum. The SOC proposes that a major impoundment at any position on a river system will cause a longitudinal shift in a given parameter (physical or biological) which will cause a discontinuity in the stream continuum. A certain distance is then required for the stream to return to its normal position in the continuum, and this is termed a 'discontinuity distance'. The effect of regulation by multiple impoundment on the 'discontinuity' (recovery) 'distances' for various physical, chemical and biological attributes of the Palmiet River (a short, steep gradient, cool, acid, low nutrient system) was investigated in a two-year study. Two zones of the river were identified for study: one below an upper-reach impoundment, Nuweberg, and one below a middle-reach impoundment, Arieskraal, as they provided sufficiently long stretches of unperturbed river (7 km and 37 km) over which recovery distances could be investigated. Sampling was undertaken monthly for 27 months from February 1986 to April 1988. Eleven sites were chosen along the length of the river: one in the pristine upper reaches, one site above and 3 sites below Nuweberg, a site on the river as it passes through the village of Grabouw, one site above and three sites below Arieskraal and a site on a tributary, the Klein Palmiet, from which water is abstracted into Arieskraal. The values of the variables downstream of the impoundment are said to increase or decrease with respect to the "above-impoundment" value. Median temperatures, pH and alkalinity increased below Nuweberg, but decreased below Arieskraal, whereas the converse was true for soluble reactive phosphate. Seasonal flow regime reversal occurred below Nuweberg and seasonal flow constancy below Arieskraal; there were seasonal shifts in temperature and a dampening of the annual temperature range below both impoundments; and seasonal shifts in alkalinity below Arieskraal. At least partial recovery was noted in all cases, but in some instances, recovery was incomplete to the estuary.

Includes bibliographical references (p. 206-231). / The use of bruchid beetles for biologicval control of mesquite, Prosopsis species, in South Africa is deemed to have failed because the beetles are supposed to be unable to compete with livestock which utilise the seed pods of mesquite extensively as forage. These assumptions have been made without any evidence as to how the beetles and livestock interact or as to whether mesquite is site or seed limited in South Africa. This study was initiated to test the hypothesis that the beetles are not coping with competition with livestock and that mesquite is site limited and not seed limited in South Africa.

Includes bibliographical references. / The construction of a portacaval shunt in the rat is followed by a series of characteristic phenomena : weight loss, hypo-albuminaemia, hyperglobulinaemia and an increase in the circulating antibacterial antibody levels to endogenous bowel micro-organisms. The weight loss is characterised by several weeks of decreasing weight followed by a slow progressive reversal to normality and it has its origins in postoperative anorexia. The hypo-albuminaemia to some extent parallels the weight loss but never reaches the same magnitude and it too is likely to be closely associated with anorexia. The hyperglobulinaemia which is polyclonal embraces a rise in all three major immunoglobulin classes of the rat. Evidence is presented that links this polyclonal hyperglobulinaemia to enhanced antibacterial antibodies which increase following the portacaval shunt. The shunt is believed to effectively separate the reticulo-endothelial system of the liver from the portal circulation thus allowing unlimited and constant access of antigenic material from the bowel to immunocompetent cells. Evidence is also advanced that such material from microorganisms may also stimulate other immune reactions. Similar studies in the pig are also presented and the close parallel with chronic human liver disease led to the development of an hypothesis that portal shunting of blood is the cause of hyperglobulinaemia in man. The rat is suggested as a suitable model for the experimental reproduction of human hyperglobulinaemia.

Bibliography: pages 170-172. / Two crab species have been exploited on the South West African/ Namibian continental slope since 1973. The deep-sea red crab Geryon maritae forms >99 percent of the catch made by traps, the balance being a by-catch of stone crab Lithodes tropicalis. Historical information dating back to the late 1970's has been examined, but most of the data analysed in this study have been collected since 1980. Most of the research has been conducted on red crab. Four aspects of its biology have been examined in some detail, namely its reproduction, growth, movements and causes of its specific dep t h zonation off Namibia. These (particularly the first two) aspects have been used, together with information from commercial sampling and catch statistics, to examine possible changes in the yield-per-recruit should the age at first capture be increased, or fishing effort reduced. On the basis of these results, some management options are presented. Several techniques (photography, trawling, effective fishing area and tag-recapture) have been used to examine the abundance and density of red crab off Namibia, and are critically compared . Research on the stone crab has been largely restricted to an analysis of commercial catch data, though an unusual symbiotic relationship with a liparid fish has been identified and discussed.