Typewritten copy / Includes bibliographical references / 1 v. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Waite Agricultural Research Institute, 1955

This study assessed the importance of overwash and breaching events on the ichthyofaunal community structure in the medium-sized temporarily open/closed Mpekweni Estuary located on the southeast coastline of southern Africa. The fish in the littoral zone of the estuary were sampled using a 5m seine net while the channel region was sampled using two nets, a smaller meshed 30m seine net to target the estuarine spawning species and the juvenile estuarine-dependant marine spawners, and a larger meshed 50m seine net to target the larger marine and freshwater spawning species. Intensive monthly sampling over two years provided data on selected physico-chemical and biological parameters. During the two year sampling period from November 2005 to October 2007 the estuary breached in late July 2006 and remained open till the sandbar re-formed across the mouth in late December 2006. Thus, sampling encompassed three open/closed phases 1) initial closed period, 2) open period and 3) re-closed period after the berm was re-formed. The open period was divided into two phases 1) the out-flow phase and 2) the tidal phase. A total of 36 fish species representing 19 families were sampled using the various seine nets employed during the investigation. In the littoral zone, the estuarine spawners (Estuarine Utilisation Category, [EUC] I), mainly the Gobiidae, Glossogobius callidus, dominated the samples numerically and by biomass. The smaller estuarine spawning species sampled in the channel were numerically dominated by Gilchristella aestuaria in conjunction with two other EUC I species, Atherina breviceps and G. callidus. The estuarine-dependant marine spawners (EUC II), however, dominated the ichthyofaunal biomass of the channel. The abundance and biomass of the larger species targeted were dominated by estuarine-dependant marine spawning species (EUC II), principally Rhabdosargus holubi. During the closed periods of the estuary, total fish abundance and biomass displayed weak seasonal patterns. The breaching event and subsequent open period was associated with a decrease in the total abundances of fish in the littoral zone and channel of the estuary, reflecting the out-flow of estuarine biomass-rich water into the marine environment. The breaching event coincided with a shift in the community composition of the ichthyofauna, reflecting the recruitment of marine spawning species into the estuary. Numerical analysis identified two distinct spatial fish communities within the estuary, a community associated with the mouth region and one comprising the rest of the estuary. The absence of any further spatial patterns in the ichthyofaunal community structure within the Mpekweni Estuary appear to be ascribed to the virtual absence of horizontal patterns in physico-chemical and biological parameters recorded in the system. Cohort analyses were employed to determine possible recruitment events for selected estuarine and marine spawning species. The estuarine spawning species displayed continuous recruitment patterns throughout the study, which appeared to be unaffected by the breaching event. Conversely, the larger marine spawning species displayed multiple cohorts, indicating non-continuous recruitment. Subsequent retrospective analysis of cohorts for the different species identified summer recruitment peaks that coincided with the breaching event and open period. Minor recruitment of marine spawning species also occurred during overwash events. The recruitment of ichthyofauna into the estuary was quantified during three distinct hydrological events: overwash, out-flow phase immediately after breaching and tidal phase during the period when the mouth was open. Estimates of fish recruitment were highest during the outflow phase immediately after the estuary breached and declined as the estuary became tidally inundated with marine water. Although not as high as the outflow and tidal phases, recruitment was evident during overwash events. Results of the current study highlight the importance of both breaching and overwashing events in structuring the ichthyofaunal community composition in a medium-sized southern African temporarily open/closed estuary. These results are broadly in agreement with similar studies conducted both locally and in other regions of the world.

The Eastern Cape contains the majority of the remaining forested areas in South Africa (95.8 percent Coastal forests and 47.6 percent Afromontane forests), however these occur in fragments. Due to the rapid rise in the human population and its needs, conversion of forests to agricultural land and the extraction of timber increases, natural vegetation are lost and this therefore leads to forests becoming fragmented into small forest patches. One of the main consequences of forest fragmentation is loss of contiguous habitat, which is the dominant threat to species globally as it negatively affects both species richness and genetic diversity. This research investigates the effects that forest fragmentation has on small mammal diversity and abundance. The study sampled small mammals in Southern Mistbelt Afromontane forest patches in the Eastern Cape. The first aim of this study was to identify which environmental variable, or combinations of variables, affect the diversity and abundance of small mammals in fragmented forest patches in the Eastern Cape during the austral summer. The second aim was to compare seasonal changes in small mammal diversity and abundance at a forest edge compared to the forest core at Beggars Bush, an Afromontane forest in the Eastern Cape, South Africa. To identify the environmental impacts that different forests have on small mammals, nine different forests were chosen in the Eastern Cape and sampled during the summer in 2013. These nine forests were: Fort Fordyce Forest, Thaba Ndoda Forest, Hogsback Forest, Dassie Kraans Forest, Langeni Forest, Burchell’s Reserve Forest, Maiden Dam Forest and Kagaberg Forest. At each site, three transects of 30 Sherman Traps each were used. Trapping periods within each forest patch lasted between three to five consecutive nights and traps were inspected once a day in the morning. Nine environmental variables were initially identified and after being tested for normality and colinearity, five variables were chosen. These variables were Altitude, Mean Annual Temperature, Gradient, Patch Size and Mean annual potential evaporation. The number of individuals captures and species richness were then incorporated as dependent variables for best subset multiple regression model selection using the Akaike Information Criterion (AIC). For the second aim, the same trapping methods were used when comparing seasonal changes to diversity and abundance within the forest core. However at the forest edge, due to the small size of the forest, only 20 Sherman traps were used in each transect with five traps (25 percent) placed in the grassland and 15 (75 percent) placed in the forest along each transect. This study was one of few to survey small mammal diversity and abundance in fragmented forests in the Eastern Cape. Gradient, patch size and mean annual potential evaporation were the variables that best predicted the individual number of small mammal captures while only gradient best explained species richness. It does however, need to be noted that capture rates and species richness were very low and this would therefore effect the analysis of environmental variables. Future studies should have a larger sample size of forest patches and include more microhabitat environmental variables to determine their effects on small mammal diversity and abundance. However, it should be noted that through climatic extinction filtering, forest mammals are resilient generalists that can tolerate fragmentation effects. Furthermore, it was found that forest edges appear to play a significant role in small mammal diversity and abundance in the Beggars Bush Afromontane forest. Some species were habitat specialists such as Rhabdomys pumilio preferring the grassland habitat and Graphiurus murinus and Aethomys namaquensis the forest habitat, while Myosorex varius was the only species that was not habitat dependant. It was found that there was a greater diversity and abundance at the forest edge compared to within the forest core throughout most of the seasons. One possible flaw was that the sampling methods were different at the edge and within the forest and therefore future studies should ensure that the method stays uniform throughout the study.

As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and Columbia torrent salamander (Rhyacotriton kezeri). Statistical models were created to analyze the effect of habitat variables on SAA occupancy, and determine whether those variables changed relative to road crossing structures. Results showed that coastal tailed frog occupancy was positively associated with dissolved oxygen and crayfish presence, negatively associated with longitude, and had a slight quadratic relationship to channel confinement. Because all sites were highly saturated with oxygen, percent dissolved oxygen was likely a surrogate for one or more other covariates, such as in-stream habitat or substrate size. Detection rates of Pacific giant salamander were too high and detection rates of Columbia torrent salamander were too low to provide reliable models, but they did provide some insight into the factors affecting occupancy in the study area, including information about their interactions with road crossing structures. Occupancy rates of Pacific giant salamanders in the study area appear to be unaffected by road crossings, fish passable or otherwise. Conversely, torrent salamanders seemed to be mostly absent from the study sites altogether, but based on the one stream where they were detected, they are not excluded from occupying fish barrier culvert sites. Top weighted habitat covariates, including dissolved oxygen, channel confinement, crayfish and fish presence, and flow constriction are all indicators of disturbance that can be linked to road crossings. Although the size and structure of road crossings did not prove to significantly influence SAA occupancy, indicators of stream disturbance that can be related to road crossings were included in the best models for predicting occupancy, demonstrating the importance of reducing disturbance related to road crossings on streams.

Thesis (MA (Geography and Environmental Studies))--University of Stellenbosch, 2006. / The Okavango river along the panhandle of the Delta, in Botswana, is home to many wildlife species as well as to many large village communities. Local communities rely on the riverine system and its resources for subsistence and commerce. Activities associated with the utilization of these resources are governed by the fluctuating water levels of the river, which inhibit access during high water levels and allow access during low water levels. The high intensity of activities, such as reed harvesting, fishing and increased tourism, during low water periods coincides with the breeding season of many wildlife species in the system, including the Nile crocodile (Crocodylus niloticus). Over 90% of crocodile breeding areas in the Delta are found only in the panhandle region. The association between the intensity of human activities in the floodplains and crocodile nesting activity means that much of the habitat required for nesting is vulnerable to human disturbance and this could have severe negative impacts on the future of the Okavango crocodile population. The study evaluated habitat vulnerability by mapping and spatially comparing habitat suitability, based on optimum environmental requirements for crocodile nesting, and human disturbance factors. A detailed crocodile nesting survey was carried out to locate and test all nesting sites according to criteria selected by species experts. The results from the survey were used to locate suitable nesting habitat in the study area by analysis in a Geographic Information System (GIS). Disturbance factors were visually identified and their locations in the study area spatially mapped. Their spatial influences on crocodile nesting were used as factors in a Multi-Criteria Evaluation (MCE) that evaluated the combined effect of the disturbances on the area defined as suitable crocodile habitat. The results indicate the extent of habitat vulnerable to human disturbances. The results from the study show that 59% of once suitable crocodile habitat is currently disturbed by human activities. Most of the remaining 41% of undisturbed habitat is located along the Moremi/Phillipa side channel, which represents a core area for protection measures to be instated. The study recommends the declaration of a crocodile nesting sanctuary in this side channel to ensure the breeding success of this keystone species.

The dispersal of freshwater fishes in the Cape Floristic Region of South Africa has been attributed to river capture events and confluence of rivers during sea level regression. The role of low drainage divides and inter-basin water transfers have received less attention. A unique lineage of Galaxias zebratus (hereafter the Joubertina galaxias) occurs in two currently isolated river systems, the Gamtoos and Krom. The present study mapped the distribution of the Joubertina galaxias and used mitochondrial and nuclear DNA sequences to assess the processes that could have influenced its current distribution pattern. Analyses of both mitochondrial cytochrome ♭ and nuclear (S7) sequences revealed that observed genetic differentiation cannot be explained by isolation between the Gamtoos and Krom River systems. No genetic differentiation was found between the Krom River System and the Twee River (a tributary of the Gamtoos River System). Shallow genetic differentiation (0.4% for cytochrome ♭ and 0.3% for S7) was found between the Krom and the remaining populations in the Gamtoos River System. High levels of genetic structuring were observed within the Gamtoos River System with most tributaries having one or more unique alleles. Inter-basin dispersal during pluvial periods or recent human mediated translocation seems to be the most plausible explanations for presence of the Joubertina galaxias in the Krom River System. The present study also assessed the threats and habitat preferences of the Joubertina galaxias, and an evaluation of the conservation status of this lineage was done. The Joubertina galaxias is threatened mainly by alien fish invasion, habitat loss and loss of genetic diversity due to fragmentation of its populations. Due to its very restricted geographic range, small known population sizes and the intensity of threats to this lineage’s survival, this lineage has been assessed as Endangered. The lineage has a restricted Area of Occupancy (AOO) and Extent of Occurrence (EOO). The extent of occurrence has declined in all tributaries and is continuing to decline in all except two tributaries that are secure. The lineage may have had natural fragmentation among its populations, but recent threats have completely isolated the populations. The threats affect the lineage’s survival potential in the four tributaries which have small populations that are not presently viable. The densities observed for the Joubertina galaxias ranged from 0.16 - 1.3 fish /m² and the number of mature individuals for the whole population seems to be less than 2500 mature individuals. There is therefore a need for specific conservation actions to ensure the long-term survival of this unique lineage.

Graduation date: 2006 / Habitat loss causes a reduction in available resources for wildlife, alters the configuration of remaining habitat, and may isolate wildlife populations. White-breasted nuthatches (Sitta carolinensis) are experiencing long-term population declines in the Willamette Valley of Oregon, where they are historically associated with oak woodlands. As secondary cavity-nesters, white-breasted nuthatches may be limited by the availability of existing cavities for nesting and roosting. Oak vegetation in the Willamette Valley has changed since European-American settlement times from vast areas of open oak savanna to isolated closed-canopy stands separated by agricultural fields. We examined nuthatch density, nest cavity selection, and nest success in relation to oak woodland structure and landscape context. We conducted point transect surveys in 3 strata: woodland interiors, large woodland edges, and small woodlands. We located and monitored nuthatch nests and sampled vegetation at nest locations and matching random locations around each nest. Woodland structure and edge density were measured at a 178-m radius (home range) scale, and landscape context was measured using vegetation cover within a 1-km radius around point transects and nests. We used program DISTANCE to fit detection functions and calculate nuthatch densities. We used conditional logistic regression to compare nest locations with random locations, and analyzed nest success with Mayfield logistic regression. White-breasted nuthatch density was significantly higher in small woodlands than in edges of large woodlands, which had higher nuthatch density than woodland interiors. Density of nuthatches increased with a combination of oak cover within a 1-km radius of the point, edge density within a 178-m radius, and number of oak trees >50 cm diameter at breast height (dbh) within a 100-m radius. Nest cavities were situated in oak trees containing more cavities than random oak trees that had cavities, and oak trees used as nest trees had a larger dbh than oak trees within random plots. Local woodland structure at nest locations was characterized by larger trees, measured by greater mean dbh, canopy cover, and basal area of oaks than random locations within the home range. Nest success in natural cavities was 71% and was not predicted by attributes of nest cavities, nest trees, local woodland structure at nests, woodland structure at the home range scale, or landscape context. These results suggest that the most suitable habitat for white-breasted nuthatches in the Willamette Valley includes oak woodlands in close proximity to one another with a high proportion of edge and mature oak trees. Managers should preserve trees containing cavities and large oak trees whenever possible. Thinning of small oaks and removal of conifers in oak woodlands to create more open, savanna-like conditions may also promote the development of larger oaks with more spreading branches, providing more opportunities for cavities to form and more foraging surface area for nuthatches.