Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The investigation of the interrelationship of the fluvial morphology and the salinity of the Great Fish River Estuary was performed by the combination of a two-dimensional morphological model and a one dimensional advection dispersion module. Two scenarios were defined for investigation, namely Scenarios A and B. Model bathymetry and grid/network for each model and scenario was compiled from topographical information obtained from aerial photos, SRTM data, LIDAR and 24 measured river cross sections of the area from the river mouth up to 27km upstream of the river mouth. Model boundary conditions were developed from empirical formulas and measured data from the Department of Water and Sanitation (DWS). Both models were calibrated with results obtained during field measurement conducted from 5 – 7 May 2012. Scenario A consisted of a long term 5 year morphological simulation (1 May 2007 to 30 May 2012) with manual mouth closure events for identified river low flow periods. Water levels upstream of the river mouth were extracted from the two-dimensional morphological module and used as the downstream boundary condition of the one-dimensional advection dispersion (salinity) model. For scenario B floods with return periods between 1:2 and 1:100 years were simulated in the morphological model. The resultant bathymetries were then used to compile the network and bathymetry of the one dimensional advection dispersion (salinity) model. The different flood resultant bathymetries were then used with equal boundary conditions (representative of the average flow in the river) in the one dimensional salinity model. The predicted salinity was compared for each bathymetry used. From model results distinct trends were observed. During low flow conditions the estuary basin fills with sediments and during floods the sediments are flushed out of the estuary. Large magnitude floods greatly erode the estuary especially in the middle reach, during floods the tidal inlet experiences overtopping and subsequent erosion, the constriction at the tidal inlet is completely destroyed during larger floods. The estuary mouth in its closed state experiences slight overtopping and the mouth is breached during periods of high river flows. The magnitude of salt intrusion depends mainly on the size (the constriction) of the river mouth (tidal inlet). During periods of mouth closure the average salinity in the estuary decreases, average salinity increases if the tidal inlet area is increased. The extent of salt intrusion is approximately 10 km upstream of the river mouth when the mouth is open and the intrusion length increases during spring tides. / AFRIKAANSE OPSOMMING: Die verwantskap tussen die Groot Vis Rivier Estuarium morfologie en sout toestand is ondersoek deur die kombinasie van ‘n twee dimensionele morfologiese model en ‘n een dimensionele sout model. Twee toestande is gedefinieer vir ondersoek naamlik Scenario A en Scenario B. Die area vanaf die rivier mond tot 27 km stroomop van die rivier mond is deur die modelle gesimuleer. Die gemodeleerde area stem ooreen met die area waar gemete rivier-snit diepte metings beskikbaar was, onbrekende data is aangevul met behulp van lugfotos, LIDAR- en SRTM- data. Die model grens toestande is bepaal met empiriese vereglykings asook gemete data vanaf die Departement Waterwese. Beide numeriese modelle was gekalibreer met veld data verkry vanaf 5 tot 7 Mei 2012. Scenario A het behels ‘n langtermyn 5 jaar morfologiese modellering (1 Mei 2007 tot 30 Mei 2012) met toemond toestande gedurende gedefinieerde rivier vloei toestande. Die watervlakke van die twee dimensionele morfologiese model stroomop van die mond is gebruik as die stroomaf grenstoestand van die een dimnesionele model om die effek van die morfologiese veranderinge te inkorporeer in die sout model. Scenario B het behels die simulering van rivier vloede met herhaal periodes tussen 1:2 en 1:100 jaar in die morfologiese model. Die rivier-bodem vlakke verkry van laasgenoemde simulasiesis toe gebruik in die een dimensionele sout model met dieselfde grenstoestande wat ooreenstem met die gemiddelde toestande in die Groot Vis Rivier. Aangesien die grenstoestande dieselfde was en net die rivier-bodem vlakke gevarieer is, kon die effek van vloede op die souttoestand in die estuarium bepaal word. Uit die model resultate kon duidelike tendense waargeneem word. Gedurende lae rivier vloei toestande is die estuarium gevul met sediment en tydens vloede het die sediment weer ge-erodeer en gedeponeer in die oseaan. Groot vloede veroorsaak baie erosie in die estuarium veral in die middel bereik en by die riviermonding. Indien die vloed groot genoeg is word die riviermond vernouing totaal uitgespoel. Die riviermonding in die geslote staat ondervind effense oorstroming en word oopgespoel indien die rivier vloei groot genoeg is. Die graad van die sout indringing in die estuarium hang hoofsaaklik af van die grootte (die vernouing) van die rivier mond. Gedurende toe mond toestande is die gemiddelde sout vlakke in die estuarium laer, wanner die rivier monding groter raak, word die gemiddelde sout vlakke in die estuarium meer. Die omvang van die sout indringing strek tot ongeveer 10 km stroomop van die rivier mond wanneer die mond oop is en die indringing afstand neem toe gedurende spring getye.

From introduction: This study is concerned with the factors responsible for mineralisation of water in the Great Fish River, in particular the irrigation return flow and groundwater seepage components. A small irrigated area in the lower Fish River Basin was chosen for a detailed study of irrigation water input, groundwater and seepage water fluctuati ons, and the affect of soils and rocks on river water mineralisation. / KMBT_363 / Adobe Acrobat 9.53 Paper Capture Plug-in

The principal objective of this thesis was to gain an understanding of the movement patterns of spotted grunter Pomadasys commersonnii, an estuarine-dependent fishery species, in the turbid, freshwater dominated Great Fish Estuary. Both manual and automated telemetry methods were used to monitor the movements of spotted grunter during two separate studies conducted in summer and spring 2003 and 2004. Acoustic transmitters were surgically implanted into twenty spotted grunter with lengths between 263 and 387 mm TL in the first study and twenty spotted grunter ranging between 362 and 698 mm TL in the second study. The specific objectives were to gain an understanding of (i) the time spent in the estuarine environment (ii) the space use and home range size, and (iii) the abiotic factors governing the movement patterns of spotted grunter in the estuary. The nursery function of estuarine environments was highlighted in this study as adolescent spotted grunter spent a significantly larger proportion of their time in the estuary than adult fish (p < 0.0001; R² = 0.62). The increased frequency of sea trips, with the onset of sexual maturity, provided testimony of the end of the estuarinedependent phase of their life-cycle. Although considered to be predominantly marine, the adult spotted grunter in the Great Fish Estuary utilised the estuary for considerable periods. Adults are thought to frequent estuaries to forage, seek shelter and to possibly rid themselves of parasites. During this study, the number of sea trips made by tagged fish ranged from 0 to 53, and the duration ranged from 6 hours to 28 days. The tidal phase and time of day had a significant effect (p < 0.05) on the sea trips undertaken by fish. Most tagged spotted grunter left the estuary during the night (84%) on the outgoing tide, and most returned in the evening (77%) during the incoming tide. Sea temperature (p < 0.0001; R² = 0.34), barometric pressure (p = 0.004; R² = 0.19) and wind (p = 0.01) had a significant effect on the number of spotted grunter recorded in the estuary. Spotted grunter were more prone to return to the estuary after high barometric pressure, when low sea temperatures (upwelling events) prevailed. There was a significant positive relationship between home range size and fish length (p = 0.004; R² = 0.20). Small spotted grunter (< 450 mm TL) appeared to be highly resident, with a small home range (mean size = 129 167 m²), that was generally confined to a single core area. Larger individuals (> 450 mm TL) occupied larger home ranges (mean size = 218 435 m²) with numerous core areas. The home ranges of small and large spotted grunter overlapped considerably yielding evidence of two high use areas, situated 1.2 km and 7 km from the mouth of the Great Fish Estuary. Tagged spotted grunter were located in a wide range of salinity, turbidity and temperature, but were found to avoid temperatures below 16 ºC. The daily change in environmental variables (salinity, temperature and turbidity) had a significant effect on the change in fish position in the estuary (p < 0.0001; R² = 0.38). The distribution of tagged spotted grunter, particularly the larger individuals, in the Great Fish Estuary was influenced by the tidal phase (p < 0.05); they moved upriver on the incoming tide and downriver on the outgoing tide. This study provides an understanding of the movement patterns of spotted grunter in the estuary and between the estuarine and marine environments. Consequently, it provides information that will assist in the design of a management plan to promote sustainability of this important fishery species. The techniques used and developed in this study also have direct application for further studies on other important estuarinedependent fishery species.

Two and a half years of data were collected from the Great Fish River and estuary using seine nets and gill nets to determine the fish species composition within these regions. The head region of the Great Fish River estuary was found to have a rich fish fauna, with the euryhaline marine fish component totally dominating the catch in all three regions. Gilchristella aesiuaria was the single most common species and several euryhaline marine species were captured in freshwater for the first time. Physical parameters were also measured in an effort to ascertain the possible factors which may affect the distribution and length frequency of the most common species within this area. Salinity was found to be the single most important factor affecting the species composition, and the sampling area was consequently divided into three regions, viz. river (< I ‰), head (1-4 ‰) and estuary (> 4 ‰). In addition, it was determined that river flow rate during the month prior to sampling also had a profound effect on species composition in all three regions. Based on the available evidence it is suggested that for most species this is related to conductivity levels rather than flow per se.

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The re-introduction of black rhinoceros onto the Great Fish River Reserve in the Eastern Cape, following the species absence for over a century, created an opportunity to study this species in the thicket biome, and in particular the succulent thicket of the Great Fish River valley. The thicket biome is quite different from the habitats in which other extant populations of these animals are found and where studies of their demography have been undertaken. Data collection occurred from May 1986, with the arrival of the first four animals to December 2008, when the population was estimated to be 144 individuals. A variety of monitoring techniques were used including direct ground observations, aerial helicopter census, aerial monitoring by microlight aircraft, camera traps and opportunistic observations, each with its own advantages and disadvantages. The combination of methods and effort has resulted in the population being recognized as completely known with up to 97% of the animals being located at least once per year with a mean frequency of sightings of 11.5 per animal per year. In 2008, the population was about 20% juvenile, 36% sub-adult and 44% adult with a female biased sex ratio of 1.3 females per male. Mean age at first birth was about 80 months and this increased significantly with increasing density of black rhinoceroses. Mean intercalf interval was about 28 months and 41% of adult females gave birth each year. Mortality rates were low for juveniles, higher for sub-adults and higher for males than females. There was a weak but significant positive effect of density on male mortality. Population growth rate was about 10% and was not significantly affected by density. These results suggest that this population is beginning to show the first indications of density dependant constraints and that harvesting should be implemented in order to maintain the productive tempo. A secondary goal of the Management Plan will then be realized as the population functions as a donor to establish founder populations elsewhere within the Diceros bicornis minor range.

Colonisation theory relative to introduced populations was examined with a view to determining the usefulness of theoretical concepts in the prediction of the success of an invasion by a species. To this end, the Great Fish River, with reference to species introduced by the Orange/Fish Tunnel, was used as a case history. It was concluded that theoretical descriptions of population growth, control and decline are useful only when considering individual ecosystems or species. The highly variable nature of species and environments nullifies attempts to simplify behavioural characteristics into a predictive framework. There is an abundance of terminology associated with introduced organisms and frequently many of these terms are used synonymously. Eleven terms have been defined in this thesis with a view to standardising terminology. Characteristics of species and environments which enhance their susceptibility to invasions by exotic ichthyofauna were discussed and summarised. Distribution data concerning exotic fish introduced into the Great Fish River by the Orange/Fish Tunnel has demonstrated that, with the exception of Clarias gariepinus, all remaining exotics have restricted distributions. Only Barbus aeneus appears to be extending its range down the drainage. Age, Growth, reproduction and condition data support the conclusion that, excluding B. aeneus and C. gariepinus, invasive species in the drainage are not performing well. Of the five invasive species (B. aeneus, Labeo capensis, L. umbratus, Gephyroglanis sclateri and Cyprinus carpio), only two have established populations (B. aeneus· and C. gariepinus). Labeo umbratus and C. carpio were present on the Great Fish River prior to the construction of the tunnel and populations of the species could not be distinguished. It was concluded that there is no evidence to suggest that exotic species introduced into the Great Fish River are having a deleterious effect on indigenous, endangered ichthyofauna. Monitoring of the drainage should be continued to ensure that a danger to indigenous species does not develop.

Using a range of satellite-derived indices I describe. monitor and predict vegetation conditions that exist in the Great Fish River Valley, Eastern Cape. The heterogeneous nature of the area necessitates that the mapping of vegetation classes be accomplished using a combination of a supervised approach, an unsupervised approach and the use of a Moving Standard Deviation Index (MSDI). Nine vegetation classes are identified and mapped at an accuracy of 84%. The vegetation classes are strongly related to land-use and the communal areas demonstrate a reduction in palatable species and a shift towards dominance by a single species. Nature reserves and commercial rangeland are by contrast dominated by good condition vegetation types. The Modified Soil Adjusted Vegetation Index (MSA VI) is used to map the vegetation production in the study area. The influence of soil reflectance is reduced using this index. The MSA VI proves to be a good predictor of vegetation condition in the higher rainfall areas but not in the more semi-arid regions. The MSA VI has a significant relationship to rainfall but no absolute relationship to biomass. However, a stratification approach (on the basis of vegetation type) reveals that the MSA VI exhibits relationships to biomass in vegetation types occurring in the higher rainfall areas and consisting of a large cover of shrubs. A technique based on an index which describes landscape spatial variability is presented to assist in the interpretation of landscape condition. The research outlines a method for degradation assessment which overcomes many of the problems associated with cost and repeatability. Indices that attempt to provide a correlation with net primary productivity, e.g. NDVI, do not consider changes in the quality of net primary productivity. Landscape variability represents a measure of ecosystem change in the landscape that underlies the degradation process. The hypothesis is that healthy/undisturbed/stable landscapes tend to be less variable and homogenous than their degraded heterogenous counterparts. The Moving Standard Deviation Index (MSDI) is calculated by performing a 3 x 3 moving standard deviation window across Landsat Thematic Mapper (TM) band 3. The result is a sensitive indicator of landscape condition which is not affected by moisture availability and vegetation type. The MSDI shows a significant negative relationship to NDVI confirming its relationship to condition. The cross-classification of MSDI with NDVI allows the identification of invasive woody weeds which exhibit strong photosynthetic signals and would therefore be categorised as good condition using NDVI. Other ecosystems are investigated to determine the relationship between NDVI and MSDI. Where increase in NDVI is disturbance-induced (such as the Kalahari Desert) the relationship is positive. Where high NDVI values are indicative of good condition rangeland (such as the Fish River Valley) the relationship is negative. The MSDI therefore always exhibits a significant positive relationship to degradation irrespective of the relationship of NDVI to condition in the ecosystem.

Invasive species are of particular concern as they have the potential to alter community structure and food web relationships within their invaded habitats. African sharptooth catfish Clarias gariepinus, a generalist predator, was introduced through an inter-basin water transfer scheme into the Great Fish and Sundays Rivers, Eastern Cape, South Africa, where it threatens the native riverine biota. This thesis assessed its impact from a trophic perspective. Patterns in catfish distribution and abundance revealed an upstream to downstream gradient that was associated with spatial distribution of most species within the mainstream, and a mainstream to tributary gradient that was associated with the spatial distribution of native minnows. The catfish was predicted to occur widely within the mainstem habitats and to decrease progressively along the mainstrem to tributary gradient with the physico-chemical environment being a good proxy for predicting both its occurrence and abundance. The results suggest the catfish proliferated within mainstem habitats where invasion resistance was possibly reduced due to alteration of flow. Population dynamics and size structuring of two native cyprinid minnows Pseudobarbus afer and Barbus anoplus, threatened by catfish, were examined within uninvaded headwater streams in relation to their proximate physical habitats. Their habitats were characterised by seasonal variation in physico-chemical conditions and a spatial variation in substrata compositions. No evidence of differences was found between seasons for density and capture probability for either species. The population size and density for P. afer was found to increase with increasing proportion of boulders. In comparison, B. anoplus population size and probability of capture increased with increasing proportion of bedrock and bank vegetation, respectively. Size structuring was explained predominantly by seasonality and habitat variables for P. afer and B. anoplus, respectively. Stable isotope ratios of carbon and nitrogen were used to compare the spatial variation in both the community-wide and catfish-specific niches and to estimate catfish prey sources from different habitats within the invaded systems. Aquatic community and catfish niches were statistically different among localities, suggesting that each locality had a distinct community-wide trophic structure. Dispersion metrics indicated no evidence of differences in the clustering among individuals, but provided evidence of differences in path trajectories for the comparisons of catfish populations that suggested dietary plasticity within different localities. Dietary studies revealed both ontogenetic shift and omnivory that suggested that catfish may exhibit less pronounced top-down effects within its invaded habitats. Manipulative experiments were used to test the response of benthic macroinvertebrates within two rivers that were differentially impacted by catfish as a presstype disturbance. Macroinvertebrates were non-responsive to catfish presence within a system where catfish had previously been established. In contrast, excluding catfish in this system indicated a response that suggested the importance of refuge within invaded habitats and the possible recovery pattern of certain macroinvertebrate taxa. By comparison, introduction of catfish within previously uninvaded localities provided evidence of direct catfish impact through elimination of conspicuous taxa. Acoustic telemetry was used to investigate catfish movement patterns within an invaded lentic habitat and provided evidence that habitat utilisation was non-random. The shallow and structured river mouth habitat, which was most utilised, was probably the most ideal for its breeding and feeding. This inferred potential overlap with native species and suggested the risk of predation and competitive interference. Catfish also exhibited both nocturnal and diurnal activity patterns that were probably related to feeding.

Very little is known about the spatio-temporal ecology of the yellow mongoose Cynictis penicillata, despite this small carnivore being widely distributed in the southern African subregion. Until the present study, activity patterns and daily movement distances had only been investigated over a single season, and information on home range sizes was only available from a few populations. Here, I aimed at determining the activity patterns and the space use of yellow mongooses over the different seasons of the year in the Great Fish River Reserve (Eastern Cape, South Africa). In addition, I tested some predictions related to environmental factors (variations in photoperiod, climatic conditions and food availability over the year), as well as life cycle (reproduction) and morphological and physiological characteristics (sexual dimorphism and thermoregulatory aspects associated to the possession of an elongated body). From September 2005 to August 2011, spatio-temporal data were collected through 102 continuous tracking sessions (84 during the day and 18 during the night) of 12 adult individuals (seven males and five females) fitted with motion-sensor radio-collars. Additional data were obtained through semi-continuous tracking sessions and random locations. Yellow mongooses were essentially diurnal and crepuscular. Activity levels averaged 57 percent during the day (n = 11,807 fixes) and only 11 percent at night (n = 3,623 fixes). Yellow mongooses emerged from their burrows on average (± SD) 85 ± 62 min after sunrise (range: –11 to +369 min) and returned 21 ± 84 min before sunset (range: –518 to +225 min). The duration of the daily activity period varied between 12 min and 15 h 36 min, with a mean of 9 h 28 min. Both sexes exhibited some overground activity after sunset, but this was most pronounced in males than in females. Nocturnal activity outside the activity period was generally restricted to short underground bouts of activity occurring at anytime of the night. Diurnal resting, with up to 11 bouts per activity period, occurred in 98.8 percent of activity periods. Overall, yellow mongooses were active during 68 ± 17 percent of the time spent outside the burrow. Photoperiod acted as a zeitgeber and activity was negatively affected by adverse climatic conditions (very hot or conversely low temperatures, rain, wet soil) and probably low terrestrial arthropod activity/availability. No intersexual difference in activity levels was found, although the higher body mass of males (on average 16 oercent) implies higher metabolic demands. The total home range size (MCP 100 percent ) averaged 0.55 ± 0.65 km2 (range: 0.10–2.36 km2) and the related total perimeter measured on average 2.80 ± 1.71 km (range: 1.17–7.36 km). Male home ranges were on average more than twice large than those of females, but this difference did not reach statistical significance. However, males had larger daily home ranges (0.13 ± 0.15 km2) than females (0.05 ± 0.05 km2). In addition, daily movement distances of males were longer (1.99 ± 1.07 km) than those of females (1.29 ± 0.66 km). Males also travelled at a faster speed (0.29 ± 0.13 km/h) than females (0.18 ± 0.07 km/h). Overall, sex clearly appeared to play a role in the spatial ecology of yellow mongooses, but the underlying explanation does not seem to be linked to sexual dimorphism (body mass) or reproductive activity. Whilst the role of food availability on the space use of yellow mongooses is unclear, it is likely that low temperatures negatively affect yellow mongoose movements, as they do for their activity levels.