Water is one of our key and indispensable natural resources. It plays a fundamental part in life (and the quality thereof), the environment, food production, hygiene, industry and power generation. Water is one of the major limiting factors in South Africa when it comes to economical growth and social development. In our country water is a scarce resource which is unevenly distributed both geographically and through time. As the demand for water increases, with increasing human populations and economic development, so to does the pollution of our river ecosystems.The Elands River is one of these natural resources that is under constant threat. It falls within the Incomati Water Management Area and is further sub divided into the Crocodile River sub area. This sub area is highly stressed, as it provides water for several human activities. The Elands River is a major tributary of the Crocodile River. The Crocodile River is a source of fresh water for several towns and is used by industry, rural and the agricultural communities (including tobacco farms). The Elands River in turn, is used for irrigation of vegetables. Both these rivers support a rich diversity of aquatic life. Along with its social and economical importance, the Elands River has immense ecological importance, as it holds great biodiversity including critically endangered biota. The main anthropogenic impacts on the Elands and Crocodile rivers include: · The Sappi Ngodwana Mill and the associated pulp and paper activities · The influence of the Ngodwana dam wall on the flow and water quality within the lower Ngodwana River · Nutrient loading taking place due to the treated sewage that is released into the river in the upper reaches and in the vicinity of the Mill · Sedimentation and flow regulation that is taking place in the Crocodile River, upstream of the confluence with the Elands River · And the agricultural activities within the Elands River system. The activities related to the Mill are the major concern in the study. The Sappi Ngodwana Mill is situated at the confluence of the Elands and Ngodwana rivers. The mill does not discharge effluent directly into the river. The effluent is however, irrigated onto the 514 hectares of farmlands adjacent to the Mill. The irrigated effluent has contaminated the groundwater in this area and the primary influence of this groundwater contamination is the deterioration of the surface water quality as well as, negatively impacts the quantity of water in the Elands River. The groundwater enters the Elands River through three springs near Ngodwana namely Fraser’s eye, Northern eye and Eye X. The groundwater from both Fraser’s eye and Eye X has been contaminated with calcium, potassium, magnesium, sulphates and most importantly chlorides. All these substances contribute to the increase in conductivity in the Elands River, which in turn may have a possible impact on the ecological integrity of the system. The pulp and paper industry is a large consumer of water and few regrettable incidents over the years have given the industry a reputation as a major water polluter. The industry’s management of water is,however, of world class and every attempted is made to manage the environment in a sustainable manner. This study aims to assess the impact of these anthropogenic activities on the associated aquatic ecosystems. Assessing the impact of anthropogenic activities on the aquatic environments, like the Elands River, has in the past been based mainly on the assessment of water quality. Earlier management of water resources has thus been based on the potability of water. Over the last decade management initiatives have expanded to include domestic, agricultural, recreational and most importantly instream (fish, invertebrates etc.) users. It has become common practise to use aquatic biota to assess the impacts of human activities of freshwater resources. The reason for this is that animals and plants can provide a long–term integrated reflection of water quality, quantity, habitat quality and other environmental conditions. Water and sediment quality was assessed by applying standard techniques and protocols. Additionally historical water quality data was obtained from the Sappi Ngodwana Mill and the Department of Water Affairs and Forestry. Habitat quality was assessed by implementation of habitat quality indices. This included that Integrated Habitat Assessment Index and the Habitat Quality Index. The vegetation at each site was identified in the field with the assistance provided by the members of the Elands River Valley Conservancy and using various field guides and the riparian zone was then demarked. The integrity of the fish community was assessed by implementing the Fish Assemblage Integrity Index and the Fish Response Assessment Index. The integrity of the aquatic macro invertebrate communities was also assessed. This was achieved through use of the South African Scoring System and the Macro Invertebrate Response Assessment Index. Finally, spatial and/or temporal trends were assessed by implementation of various multi variate statistical procedures. / Prof. J.H.J. Van Vuren Prof. V. Wepene

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. Johannesburg, 2016. / Resource selection by animals is a hierarchical process, reflecting the spatio-temporal heterogeneity in biotic and abiotic environmental conditions and resources. In savannah ecosystems, the availability and nutritional quality of forage resources across the seasonal cycle constitute two of the main drivers of feeding choices, seasonal movements, and, ultimately, population dynamics of large herbivores. As a consequence of the increasing insularisation of protected areas in southern Africa, the understanding of the ecological requirements of confined populations of nomadic ungulates constitutes a crucial issue for their management. The study aimed at determining the effects of forage quality and availability across the seasonal cycle on the home range occupation and resource selection by eland in an insular-like protected area, the Kgaswane Mountain Reserve (KMR) in South Africa. I focused on three spatio-temporal scales of selection: seasonal home range selection over the available landscape; habitat selection within the seasonal home range; and selection for plant species included in the diet. The main objectives at the scales of landscape and habitat selection were: 1) to determine the extent and location of the seasonal home ranges utilised by collared adult female eland in the KMR, in order to identify the seasonally favoured resource units within the available landscape; and 2) to determine the influence of environmental drivers, including the seasonal variation in forage quality and abundance, on resource selection by eland at the two different scales. Four adult female eland were fitted with GPS collars, over the course of two years. The extent and location of annual and seasonal home ranges were estimated using a-LoCoH. The influence of environmental factors, including vegetation-type, burnt areas, and NDVI, on landscape- and habitat-scale selection of used locations at peak feeding times over available scattered points was tested using mixed-effects logistic regression models. Despite the small size of the KMR, eland occupied spatially distinct dry and wet season ranges. The dry season ranges were smaller than their wet season counterparts, and During the dry season, seasonal ranges were small, and were located in moderate to very green (as indicated by NDVI values) woodland areas in respect to the available landscape. Eland selected for dry grassland, wet grassland, and open shrubland (associated with low NDVI levels) during the wet season, when they coalesced into a nursery herd and occupied a relatively large home range. The selective use of burnt areas over the available landscape units was mostly restricted to the wet season, after a green herbaceous flush had been prompted by rainfall events. Within the seasonal home ranges, eland preferentially foraged on burnt woodland and open shrubland, where re-growth of woody plants was also available. The study animals also selected for locations characterized by low vegetation greenness and biomass as a consequence of the concentration of foraging activities in open areas where low-lying browse was accessible. At the smallest scale considered for this study, the two main objectives were: 1) to determine the changes in the use of vegetation types and burnt areas during foraging activities between two different seasons; 2) to determine forage selection at the plant species scale, as influenced by the phenophase of grasses and browse. In March-April 2015 (wet-early dry transition season) and July-August 2015 (mid-dry season), feeding sites of eland were located through both VHF-tracking and scanning from vantage points. Characteristics of used feeding sites were only descriptively addressed, and included vegetation type, burning, canopy cover, and soil catenal position. The greenness and basal cover of plant species were also recorded. Availability, acceptance, and dietary contribution for each species were calculated for the two seasons, while the influence of phenological traits on plant species selection was investigated through mixed-effects logistic regression models. Woody plants were consumed in larger proportions than grasses and herbaceous forbs during the entire study period. Woody forbs and shrublets such as Lippia javanica and Athrixia elata were particularly favoured. Eland targeted species offering high proportions of green leaves. During the wet-early dry transition, the deciduous Vangueria parvifolia was particularly selected for, while the consumption of evergreen species, including Searsia lancea, increased during the dry season. Most of the observed grazing took place on flushing burns during the wet-early dry transition. The decline in grass consumption was paralleled by a considerably lowered use of the burns and of the dry grassland during the dry season, as also reflected by collars data. The results indicated that eland in the KMR adjusted their landscape and habitat selection in response to spatio-temporal variations in the availability and quality of food resources. During the wet season, flushing burns provided accessible green forage to nursery herds. Conversely, evergreen woody plants probably represented a crucial resource for eland during the limiting dry season, when herbaceous plants were mostly dormant and foliage on deciduous species was unavailable. Therefore, environmental heterogeneity at different spatial scales likely constitutes a key factor for the persistence of eland populations in small, fenced reserves. / LG2017

M.Sc. / The Elands River (Incomati System, Mpumalanga) is a biologically diverse and ecologically important riverine system. In terms of the South African National Water Law, the river can be regarded as an aquatic resource, with social, ecological and economical benefits to the local population and the environment itself. The ecological status of the system has, however been questioned, whereby concerns relating to the water quality and the ecological health of the Elands River has been raised. Initially, the concerns focused on an accidental industrial spill of “black liquor” into the Elands River by the Paper Mill at Ngodwana. Subsequently the groundwater in the vicinity of the Ngodwana Mill has possibly been contaminated with chlorides. The contaminated subsurface water has been discharged into the river, and is suspected to be impacting, primarily in the form of increased salinity, the integrity of the Elands River. This study assessed the ecological integrity of a segment of the Elands River between Waterval- Boven and the confluence of the Elands River with the Crocodile River. In addition this study investigated the possibility that increased chloride-based salinity levels were the factors affecting the ecological integrity of the Elands River. The study is divided into three main components. The environmental component involves the assessment of the surface water quality and flow, physical profile, current aquatic habitat status and a biotic integrity assessment of the Elands River and the Crocodile River directly above and below the confluence with the Elands River. An ecotoxicological component incorporated a bioassay of selected chloride-based salts, using daphnids and selected fish species as test organisms. Finally an Ecological Risk Assessment was carried out to evaluate the likelihood that adverse effects were impacting on the Elands River, as a result of the activities of the Ngodwana Mill. The water quality was assessed by implementing the methodology for the determination of present ecological status: water quality, as part of the preliminary determination of the ecological reserve. Historical water quality data were obtained from the Department of Water Affairs and Forestry and from Sappi. During the study, current water quality parameters were obtained from Sappi and parameters were independently sampled. Analyses of the water quality indicated that the Elands River has been subjected to eutrophication and increased levels of chloride-based salinity. Habitat integrity was analysed by constructing two dimensional site transects of the riparian zone and instream channel. Additional habitat indices, the Integrated Habitat Assessment System, the Habitat Cover Ratings and the Site Habitat Integrity system were applied. Habitat results indicate that the in stream habitats of the Elands River are abundant and linked to the flow regime. Additionally the assessments indicated that the habitat makeup of the Elands and Crocodile rivers is primarily riffle, run and rapids habitats, which facilitate the requirements of numerous invertebrate and vertebrate aquatic communities. Biotic assessments studied the integrity of the vegetation, invertebrates and ichthyofaunal communities. The integrity of the vegetation community was assessed by implementing the Riparian Vegetation Index. Results indicated that the riparian vegetation community was modified in varying degrees due to the encroachment of exotic and terrestrial vegetation elements and by anthropogenic activities. The integrity of the invertebrate communities were assessed by implementing the South African Scoring System. Results indicated that the integrity of the invertebrate community was exceptionally high in the vicinity of Hemlock. The invertebrate community structure changed however in areas were a water quality contamination was observed. The ichthyofaunal attributes were assessed by implementing the Fish Assemblages Integrity Index and the Sensitivity Weighted Index of Biotic Integrity. The ichthyofauna assessment revealed two aspects that have conservation importance. These aspects are the occurrence of an endangered species, Chiloglanis bifurcus, and a potentially geologically isolated subspecies of Labeo-barbus polylepis. The index results indicated that the ichthyofauna community structure followed similar trends to the invertebrates by responding to the mentioned stressors. Toxicological assessments were carried out using the standard Daphnid 48-hour LC50 and fish 96-hour LC50 tests. The species selected for the tests were the currently recognized test organisms (Daphnia pulex and Poecilia reticulata) in South Africa. Additional fish species were included in the tests, these species were Oreochromis mossambicus and Clarias gariepinus. Chloride-based salts were selected as the toxicants; these included calcium chloride, magnesium chloride, potassium chloride and sodium chloride. The tests were carried out under controlled conditions using standardised protocols. Results indicated that in excess, chloride-based salinity is toxic to invertebrate and vertebrate organisms. Additionally findings indicated that potassium chloride was the most toxic and sodium chloride the least toxic of the salts. Calcium chloride was selected as the most representative salt to represent salinity. The Ecological Risk Assessment was implemented after international and national frameworks were considered. The assessment was primarily based on the results obtained from the integrity assessment of the Elands and Crocodile rivers. Results obtained indicated that the localised biological template of the Elands River, in the vicinity of the Ngodwana Mill is moderately impacted by the activities of the Mill. The impact is primarily associated with the increased salinity content of the Elands River. Effects of the stressors were modified in relation to a dilution effect. Risks posed by the stressors are deemed to be restricted to a localised area, and it is highly improbable that the stressors would result in the loss of the biotic diversity and thus the ecosystem of the Elands River as a whole. Should the current situation prevail, the intensity and spatial extent or distribution of the stressor could increase. / Dr. V. Wepener

The South African National Water Act (NWA) (No. 36 of 1998) recognises that in order to sustain the goods and services that are provided by rivers and their associated biological communities, it is necessary to conserve the entire aquatic ecosystem. Conservation and maintenance of ecosystem functioning entails the protection of the biotic components (i.e. fish, macroinvertebrates, riparian vegetation, etc.) and ensuring that the abiotic driver aspects (i.e. required amount and variability of flow, water quality and fluvial geomorphology) are addressed and met (Malan and Day, 2003). According to the Reserve Determination methodology (DWAF, 2003), sustainable utilisation of the river resources requires proper, responsible management and that exploitation without understanding or limits, impacts negatively on the ecological processes, functions and communities, both in the present and the future. Manipulation of the flow regimes of rivers, to provide water when and where people need it, has resulted in a growing deterioration in the condition (health) of riverine ecosystems (King et al., 2000). Stressors on aquatic ecosystems originating from these anthropogenic activities, include point and non-point loadings, land use influences and changes, and stream modification. These are usually defined by the drivers of aquatic ecosystems namely the geomorphology, hydrology and water quality. In turn, the effects on the physical habitat and water quality have both direct and indirect effects on the biotic communities present and are usually defined by biological responses to these changes (Kleynhans et al., 2005). There is currently limited data available to formally propose a methodology to quantify the significance of altered flows in riverine ecosystems brought about by the abstraction or excessive release of water by industrial activities on a reach scale. The aim of this study was to determine the degree and magnitude of habitat-flow alterations caused by pulp and paper mill activities in the Elands and Mvoti Rivers and to link the related biological responses to them. / Prof. V. Wepener

A research report submitted to the Faculty of Science, University of Witwatersrand, in partial fulfilment of the requirements for the degree of Master of Science (Resource Conservation Biology). Johannesburg, 2015 / The vegetation of the Kgaswane Mountain Reserve, in North West Province, South Africa, was mapped according to seven vegetation structure types, based on tree density and height, and grass height. Free-living ticks were collected by drag-sampling the vegetation from each structure type in November 2014, prior to the onset of the summer rains, and February 2015, once most of the seasonal rains had fallen. Eland (Taurotragus oryx) location information was recorded from four GPS collared cows over the two sample periods. Tick abundance was consistently lower in shorter, open, more exposed vegetation structure types, and higher in more sheltered types. Position higher up in the landscape nullified the positive impacts of trees on beneath-canopy microclimate in tall open woodlands, as indicated by comparatively lower tick numbers than in more sheltered woodland types. Tick abundance is influenced by vegetation structure and the availability of hosts. The majority of ticks trapped during both periods were larvae, with nymphs mostly present in November and adults mostly present later in the season, indicating the seasonal nature of tick cohort recruitment. Eland calving behaviour centred on areas with low adult tick abundance. Eland did not respond to total tick abundance during either sampling period. They did select areas with low adult tick abundance, and avoided areas with high adult tick abundance. This corresponded with an improvement in upland forage quality, which allowed them to avoid foraging in areas with high adult tick abundance. It is plausible that the potential for infestation by adult ticks may be a supplementary influence driving the use of space by eland.

No description available.

Habitat loss and fragmentation is a crisis affecting wildlife worldwide. In Tanzania, East Africa, a dramatic and recent (<80 years) expansion in human settlement and agriculture threatens to reduce gene flow among protected areas for many species of large mammals. Wildlife linkages can mitigate population isolation, but linkage designs lacking empirical justification may be controversial and ineffective. Connectivity conservation requires an understanding of how biogeographic factors shaped gene flow prior to habitat loss or fragmentation, however the history of interaction among populations is rarely known. The goal of my study was to provide context for connectivity conservation in central and southern Tanzania by identifying landscape features that have shaped gene flow for three ungulate species with different dispersal capabilities. I investigated historical patterns of connectivity for Maasai giraffe (Giraffa camelopardalis tippelskirchi), impala (Aepyceros melampus), and eland (Tragelaphus oryx) by estimating genetic structure among four to eight protected areas per species. Genetic structure changes very slowly among large populations and thus is likely to reflect historical processes instead of recent anthropogenic influences. I collected noninvasive DNA samples and generated microsatellite genotypes at 8 to 15 loci per species, then estimated genetic diversity metrics (allelic richness, AR, and expected heterozygosity, H[subscript E]) for each population (defined by reserve). I also calculated genetic distance (F[subscript ST] and Nei's unbiased genetic distance, D[subscript hat]) and an estimate of gene flow (Nm) between all population pairs for each species. To elucidate the possible causes of genetic structure between these populations, I tested for isolation by distance and isolation by resistance based on a suite of biogeographic factors hypothesized to affect gene flow. To do this, I created GIS-based resistance surfaces that assigned different costs of movement to landscape features. I created one or more resistance surfaces for each hypothesis of landscape effect. I used circuit theory to estimate the cumulative resistance between each pair of reserves for each weighting scheme, and then performed Mantel tests to calculate the correlation between these resistances and the observed population pairwise genetic distances (D[subscript hat]). I chose the optimal resistance model for each species as the model that was most highly correlated with observed genetic patterns. To verify that the correlation of resistance models with genetic distance was not an artefact of geographic distance, I performed partial Mantel tests to calculate correlation while controlling for the effect of geographic distance. Finally, I compared historical gene flow patterns to the distribution of contemporary human activity to predict areas that are at risk of a loss of connectivity. Indices of genetic diversity were moderate for all three species and comparable to previously reported values for other savannah ungulates. Diversity (both H[subscript E] and A[subscript R]) was highest in eland and lowest in giraffe for these populations, and was not consistently correlated with reserve size as has been reported for other species in East Africa. Although patterns in genetic distance were broadly similar across all three species there were also striking differences in connectivity, highlighting the importance of cross-species comparisons in connectivity conservation. At this scale, resistance models based on slope strongly predicted population structure for all three species; distance to water was also highly correlated with genetic distance in eland. For all three species, the greatest genetic distances occurred between populations separated by the Eastern Arc Mountains, suggesting that the topography of this area has long acted as a barrier to gene flow, but this effect is present in varying degrees for each species. I observed high levels of historical gene flow between centrally located populations (Ruaha National Park and Rungwa Game Reserve) and those in the southwest (Katavi National Park and Rukwa Game Reserve). Although human settlement in this area has been low relative to other areas, the connection between the Katavi/Rukwa and Ruaha ecosystems may be threatened by increased human activity and warrants conservation. High levels of historical gene flow were also seen between reserves in the northeast (Tarangire National Park, Swagaswaga Game Reserve) and the central and southwest populations. These connections appear highly threatened due to current land use practices, and may have already suffered a loss of gene flow. Field surveys in the lands surrounding the northeastern reserves are needed to quantify current levels of connectivity and determine whether corridors could be established to maintain or restore gene flow with other reserves. / Graduation date: 2012