OpenUCT :: Browsing by Author "Underhill, Leslie G"

Browsing by Author "Underhill, Leslie G"

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Open Access
The address sort and other computer sorting techniques
(1971) Underhill, Leslie G; Troskie, Casper G
Originally this project was to have been a feasibility study of the use of computers in the library. It soon became clear that the logical place in the library at which to start making use of the computer was the catalogue. Once the catalogue was in machine-readable form it would be possible to work backwards to the book ordering and acquisitions system and forwards to the circulation and book issue system. One of the big advantages in using the computer to produce the catalogue would be the elimination of the "skilled drudgery" of filing. Thus vast quantities of data would need to be sorted. And thus the scope of this project was narrowed down from a general feasibility study, firstly to a study of a particular section of the library and secondly to one particularly important aspect of that section - that of sorting with the aid of the computer. I have examined many, but by no means all computer sorting techniques, programmed them in FORTRAN as efficiently as I was able, and compared their performances on the IBM 1130 computer of the University of Cape Town. I have confined myself to internal sorts, i.e. sorts that take place in core. This thesis stops short of applying the best of these techniques to the library. I intend however to do so, and to work back to the original scope of my thesis.
Open Access
Biplot graphical display techniques
(1991) Iloni, Karen; Underhill, Leslie G
The thesis deals with graphical display techniques based on the singular value decomposition. These techniques, known as biplots, are used to find low dimensional representations of multidimensional data matrices. The aim of the thesis is to provide a review of biplots for a practical statistician who is not familiar with the area. It therefore focuses on the underlying theory, assuming a standard statisticians' knowledge of matrix algebra, and on the interpretation of the various plots. The topic falls in the realm of descriptive statistics. As such, the methods are chiefly exploratory. They are a means of summarising the data. The data matrix is represented in a reduced number of dimensions, usually two, for simplicity of display. The aim is to summarise the information in the matrix and to present a visual representation of this information. The aim in using graphical display techniques is that the "gain in interpretability far exceeds the loss in information" (Greenacre, 1984). A graphical description is often more easy to understand than a numerical one. Histograms and pie charts are familiar forms of data representation to many people with no other, or very rudimentary, statistical understanding. These are applicable to univariate data. For multivariate data sets, univariate methods do not reveal interesting relationships in the data set as a whole. In addition, a biplot can be presented in a manner which can be readily understood by non-statistically minded individuals. Greenacre (1984) comments that only in recent years has the value of statistical graphics been recognised. Young (1989) notes that recently there has been a shift in emphasis, among statisticians towards exploratory data analysis methods. This school of thought was given momentum by the publication of the book "Exploratory Data Analysis" (Tukey, 1977). The trend has been facilitated by advances in computer technology which have increased both the power and the accessibility of computers. Biplot techniques include the popular correspondence analysis. The original proponents of correspondence analysis (among them Benzecri) reject probabilistic modelling. At the other extreme, some view graphical display techniques as a mere preliminary to the more traditional statistical approaches. Under the latter view, graphical display techniques are used to suggest models and hypotheses. The emphasis in exploratory data techniques such as graphical displays is on 'getting a feel' for the data rather than on building models and testing hypotheses. These methods do not replace model building and hypothesis testing, but supplement them. The essence of the philosophy is that models are suggested by the data, rather than the frequently followed route of first fitting a model. Some work has gone into developing inferential methods, with hypothesis tests and associated p-values for biplot-type techniques (Lebart et al, 1984, Greenacre, 1984). However, this aspect is not important if the techniques are viewed merely as exploratory. Chapter Two provides the mathematical concepts necessary for understanding biplots. Chapter Three explains exactly what a biplot is, and lays the theoretical framework for the biplot techniques that follow. The goal of this chapter is to provide a framework in which biplot techniques can be classified and described. Correlation biplots are described in Chapter Four. Chapter Five discusses the principal component biplot, and the link between these and principal component analysis is drawn. In Chapter Six, correspondence analysis is presented. In Chapter Seven practical issues such as choice of centre are discussed. Practical examples are presented in Chapter Eight. The aim is that these examples illustrate techniques commonly applicable in practice. Evaluation and choice of biplot is discussed in Chapter Nine.
Open Access
Birds along a transect across KwaZulu-Natal: altitudinal preference and altitudinal migration
(2018) Scott, Tanya; Underhill, Leslie G
The special ornithological advantage of KwaZulu-Natal is the massive altitudinal gradient between the coastline and the Drakensberg Mountains, an altitudinal range in excess of 3000 m. It is one of the best places in the world to study altitudinal bird migration. This dissertation uses the bird data from the Second Southern African Bird Atlas Project (SABAP2), and altitudinal data from a Digital Elevation Model to try to understand altitudinal migration in a band of KwaZulu-Natal between 29°S and 30°S. The bird atlas provides data on a five minute grid, grid cells with sides of c. 9km, known as pentads. The Digital Elevation Model gives spot heights at 0.5 minute intervals. It therefore provides 100 altitudes in each pentad. There is a description of the data analysis approach used to relate bird species abundance to altitude and selected examples to show how the method works, illustrating the strengths and weakness of the approach. The developed method is then applied to the study area to investigate altitudinal migration. For each of the 304 species which occur with some regularity in the study area, the altitudinal height preferences in summer and winter are plotted and compared. Some species, such as African Dusky Flycatcher, are definite altitudinal migrants, and some species are definite residents having essentially identical altitudinal distributions in summer and winter, such as Black-bellied Starling. There are also many intermediate strategies. Numerous species have been proposed as altitudinal migrants in KwaZulu-Natal. These claims are evaluated against the results obtains in this dissertation. For some species, the suggestion that they are altitudinal migrants is clearly incorrect, and for other species the hypotheses are confirmed by the bird atlas data. The project attempted to determine if there were common factors that helped explain which species engaged in altitudinal migration. A set of life history characteristics for each species, including aspects such as diet, mass, habitat, etc, was used to evaluate if there was a relationship between the extent of altitudinal migration and these explanatory variables. No meaningful relationships were found. Explanations of altitudinal migrations therefore remain an enigma.
Open Access
Camera traps as sensor networks for space-time exploration of terrestrial mammal communities
(2018) Bussière, Elsa Marion Sylvie; Underhill, Leslie G; Distiller, Greg
Most of the conservation issues which ecologists are called on to help resolve are essentially about ecological communities. Camera trapping technology has led to a surge in the collection of large ecological datasets, which provides an unmissable opportunity to attain deeper knowledge of animal community assembly and structure. Using extensive camera trap data, this thesis examines whether camera traps can be used as sensor networks for a space-time exploration of the terrestrial mammal community that occurs in the Little Karoo of South Africa. In Chapter 1, the species-habitat relationship along a ruggedness gradient was studied. Using resource selection functions and multivariate statistics, this chapter showed that the strength of affinities, which mammals developed with specific terrain roughness, varied among species. It also enabled the recognition of subtle and continuous nuances in the spectrum of habitat preferences, providing a novel tool to explore the forces driving species coexistence in local animal communities. The theme of Chapter 2 was to consider patterns of seasonal occurrence within species circadian rhythms. Using kernel density functions with descriptive and multivariate statistics, this chapter showed that most mammal species responded to the ecological variability brought about by seasonality by adjusting their diel activity rhythms between winter and summer, resulting in a reduction of time exposure to a physiologically stressful environment caused by high temperatures in summer. It also highlighted that while some shifts only result from photoperiodism alignment, most are driven by other factors too. Chapter 3 examined temporal-partitioning as a mechanism driving sympatry. Using kernel density functions and mutivariate statistical analyses, this chapter enabled subtle nuances in the spectrum of diel activity rhythms to be visualised, highlighting the variety of temporal niche breadths and of activity onset/offset timings, which allowed diel activity rhythms to diversify and the mammal community to partition the temporal resources. Finally, in Chapter 4, topics dealing with leopard habitat preferences and leopard population density were explored. Using spatially explicit capture-recapture models, this chapter showed that leopard density remained low but varied with topographic relief; it increased with ruggedness of the terrain up to an optimum, and followed a reversed trend as the terrain roughness kept increasing. The population was composed of two groups of individuals with significantly different home range sizes, potentially explained by gender duality in movement. The chapter provided leopard density estimates ranging from 0.49 to 0.82 individual per 100 km2 . Local communities, such as that of the mammal species of the Little Karoo, are neither closed nor isolated. Therefore, it would be insightful if future studies were to embrace the metacommunity concept and explain these patterns of species distribution, abundance and interaction at multiple scales of spatio-temporal organisation.
Open Access
Citizen science reveals complex changes in barn swallow phenology in South Africa over three decades
(2016) Burman, Marc Sebastian; Underhill, Leslie G; Altwegg, Res; Erni, Birgit; Remisiewicz, Magdalena
Palearctic migrants, including barn swallows Hirundo rustica, responded to climate change in Europe from the mid to late 1900s with phenological changes, mostly showing earlier arrival and start of breeding. During this period, barn swallows in the Palearctic exhibited variable patterns of change in the timing of their arrival, breeding and departure from the breeding grounds. At the South African non-breeding grounds, the timing of migration shifted between the 1980s and 2000s, again with geographic variability. To explain these changes further, I examined geographic and temporal variability in the timing of flight feather ('primary') moult, and trends in body weight, in barn swallows ringed in South Africa between 1986 and 2012. Citizen science bird ringing, started in South Africa in 1948, generated all the data used in this project. All data were obtained from the South African Bird Ringing Unit (SAFRING).
Open Access
Ecology of the Verreaux's eagle Aquila verreauxii in natural and agriculturally transformed habitats in South Africa
(2016) Murgatroyd, Sarah Megan; Underhill, Leslie G; Amar, Arjun
Agricultural transformation generally has a negative impact on biodiversity. Owing to landscape fragmentation and reduced prey availability, predators that inhabit transformed areas are usually forced to increase hunting effort or diversify their diet and this can have negative consequences for fitness or demographic parameters. Agricultural landscapes are therefore rarely considered important in the conservation of top predators. The Verreaux's eagle Aquila verreauxii has experienced loss of natural habitat due to agricultural transformation through much of its range. Despite the conspicuous nature and widespread distribution of Verreaux's eagles in sub- Saharan Africa, there is a paucity of information on the mechanism behind the recently observed population declines of this species, which have resulted in the recent re-classification as "Vulnerable" (from "Least Concern") in South Africa. This thesis aims to explore how land transformation influences changes in several key ecological components and demographic parameters, namely breeding performance, diet and movement ecology. In this thesis, I study two geographically adjacent populations of Verreaux's eagles; one located in a natural area (Cederberg) and one in an agriculturally transformed area (Sandveld), in the Western Cape Province, South Africa, from 2011-2014. I investigate the breeding performance of the two populations. In contrast to what was anticipated I found that breeding productivity was 2.7 times greater in the agricultural than in the natural area. Population modelling suggested that in isolation the Cederberg population is unlikely to be self-sustaining, whereas the eagles breeding in the Sandveld region are likely to be acting as a source population. However, I did not have any information about juvenile or adult survival in either area. Contrasting survival rates could distort these results and are in need of further research. Verreaux's eagles are generally regarded as dietary specialists. I therefore investigated the diet composition of eagles in the two study areas as a proxy to better understand prey availability and to look for evidence of behavioural flexibility to different availability of prey resources. The relationship between diet breadth and breeding performance was explored locally and regionally using data from previous studies. Eagles in the Sandveld were found to have a more diverse diet than eagles in the Cederberg, which rely on their traditional prey, rock hyrax Procavia capensis. Theory on specialist predators assumes that diet diversification will cause reduced breeding performance. In particular, individuals within a species with more diverse diets due to reduced availability of primary prey species can display reduced breeding performance. In direct contrast to this, eagles with broad diet did not exhibit trends for reduced breeding performance, both locally and across southern Africa.
Open Access
The effects of human disturbance on the seabirds and seals at sub-Antarctic Marion Island
(2009) Wheeler, Mariette; De Villiers, M S; Underhill, Leslie G
Animals at Marion Island can be affected by logistic disturbance (especially helicopter noise), incidental pedestrian disturbance and research disturbance. The responses of wandering albatrosses (Diomedea exulans) and king penguins (Aptenodytes patagonicus) were investigated through standardised pedestrian approaches. Intensity of behavioural responses and levels of prolactin (females only) indicated that adult wandering albatrosses had become sensitised by high levels of chronic disturbance. Responses were greatest during the Prospecting and Early Incubation phases. Frequency of disturbance did not influence behavioural responses, but birds visited most often over three consecutive days had the lowest chick survival. Guarding king penguins were less likely to move away during disturbance than non-breeding groups. Visit duration and approach distance affected behavioural responses. There was evidence of habituation by king penguins to current levels of incidental disturbance. Grey-headed albatross (Thalassarche chrysostoma) adults and chicks showed short-term behavioural responses to research disturbance, and recovery times were variable. Level of chronic disturbance did not explain breeding success differences between colony sections. Instantaneous scans or counts of guarding and brooding gentoo penguins (Pygoscelis papua), incubating Crozet shags (Phalacrocoraxmelanogenis), pre-fledging grey-headed albatross chicks and non-breeding king penguins were made before and during helicopter operations.
Open Access
Factors impacting the breeding success of African penguins Spheniscus demersus on Robben Island
(2016) Tol, Leanne; Underhill, Leslie G; Barham, Peter; Sherley, Richard
The African penguin Spheniscus demersus is a seabird endemic to the south-western coast of Africa and can be found in three main breeding localities; southern Namibia, the Western Cape and Algoa Bay, Eastern Cape, South Africa. The African penguin has been listed as Endangered since 2010, having experienced a decline in population of more than 50% over the past three generations. This study was conducted at the breeding colony on Robben Island, South Africa, and examined two factors that have the potential to affect breeding success of African penguins; body mass at the onset of breeding and the suitability of various nest types to mitigate changing climatic conditions. Body mass was measured by recording weights using an automated weighing scale set up in front of a nest. Weights were taken at the start of breeding of each penguin in a breeding pair and these weights were compared to the number of chicks fledged, fledging period, hatching success, clutch size, and chick fledging weight. Hatching success, clutch size, and fledging weight were not influenced by the mass of either parent. There was a trend of shorter fledging periods as the mass of the heavier parent increased. The greatest effect was from the body mass of the lighter parent on the number of chicks that fledged from the nest; as the mass of the lightest adult increased, more chicks were fledged. If the lighter adult weighed below 2 kg there were always no chicks at the nest that fledged. This suggests evidence for a carry-over effect of body mass from the time before breeding starts into the breeding season, and highlights the importance of food availability for African penguins on a global scale, and not just a local one. The proportion of nest failures of six nest types (vegetation, open, natural burrow, building, wooden nest box, and artificial fibreglass burrow) at the incubation and chick-rearing stage were compared to rainfall and maximum temperature.
Open Access
Factors influencing the foraging behaviour of African Penguins (Spheniscus demersus) provisioning chicks at Robben Island, South Africa
(2016) Campbell, Katrina; Underhill, Leslie G; Sherley, Richard B; Steinfurth, Antje; Crawford, Robert J M
Urgent and effective conservation is needed to halt the declines of endangered African Penguins. A purse-seine fisheries closure zone was in place out to 20 km around Robben Island for three years. It provided an opportunity to investigate penguin foraging behaviour in relation to estimated local prey abundance and other factors without the confounding variable of local fishing. Penguins provisioning chicks were equipped with GPS temperature depth devices for a foraging trip. Dive data (N = 75) and GPS tracks (N = 78) were collected from 78 penguins. Of those, 14 penguins were at-sea within two days of a fine-scale hydro-acoustic pelagic fish survey. Diet sampling, breeding success and chick body condition monitoring took place in the colony. Nests were followed to outcome. Morphological indicators were developed for sex determination and body condition. Intrinsic factors, brood mass, prey abundance, wave height and direction were explored in respect to foraging behaviour. Kernel density analysis identified foraging areas, confirming consistent use of the closure area. Annual differences in foraging effort were explained by variation in local prey abundance. The time the penguins spent diving and the distance travelled from the colony were negatively related to local prey abundance. There was greater variation in foraging distance when prey abundance was lower. Foraging areas and dive behaviour were similar for the sexes. The survival of chicks in the foraging study did not differ from chicks monitored in the colony for breeding success (control chicks). The trips of penguins with nesting success (N = 44) were on average 4.5 km closer to the colony than the penguins that had nesting failure (N = 21). Chick body condition in the colony was positively related to the Anchovy (Engraulis encrasicolus) mass percentage in the diet and the local pelagic fish abundance; condition was predicted to vary by 245% over the range of local fish abundance observed during the study period (0.5 to 187 thousand tonnes). Identifying ways to avoid depletion of prey resources around penguin colonies is important for conservation of the species.
Open Access
Foraging efficiencies and species' distributions : an explanation of the Hadeda ibis (Bostrychia hagedash) in relation to soil moisture
(2008) Duckworth, Greg; Underhill, Leslie G; Altwegg, Res
The influence of soil moisture on the foraging time needed to meet BMR (foraging efficiency) in hadedas was explored in Cape Town, South Africa. This was done by monitoring hadedas foraging and recording the prey items eaten successfully per minute on soils of different moisture. BMR was calculated using a published method and diet calorimetry was used to determine the amount of energy in their diet. Results indicate that hadedas are able to forage most efficiently at intermediate soil moistures (0.40 -0.80 cm³.cm-³) whilst at either low or high soil moisture they are less efficient.
Open Access
Impacts of environmental change on large terrestrial bird species in South Africa: insights from citizen science data
(2012) Hofmeyr, Sally D; Underhill, Leslie G; Barnard, P
Large terrestrial bird species, especially cranes and bustards, have adapted to low intensity agriculture to varying degrees, but large-scale industrial agriculture is in general inimical to these species. Cranes are charismatic and well studied, but bustards are retiring and in general cryptically coloured, and little is known of most species. Of South Africa's 10 bustard species, two are endemic and three subspecies are endemic or near-endemic. Six species are threatened or near-threatened. Three crane species occur in South Africa, one of which is near-endemic; all are threatened. This thesis used data from two long-term public participation bird monitoring projects to improve our understanding of six of these 13 species. The first and second Southern African Bird Atlas Projects (SABAP1, 1987-1992, and SABAP2, 2007-) provide two sets of presence/absence data which can be compared. The Coordinated Avifaunal Roadcounts (CAR; 1993-) project provides roadcount data spanning a similar period.
Open Access
Long-term population trends and habitat preferences of waders at Strandfontein wastewater treatment works
(2016) Essig, Erica Carla; Picker, Michael D; Underhill, Leslie G; Whitelaw, Dave
The aims of the dissertation are to describe long term migrant and residential wader population trends at Strandfontein, and to identify the potential factors which influence local wader abundance. Once identified, these factors are integrated into a management plan that would create ideal wader habitat, and attract larger numbers of waders to Strandfontein.
Open Access
The moult and migration strategies of Lesser Sand Plover, Greater Sand Plover and Terek Sandpiper
(2018) Jackson, Colin; Underhill, Leslie G; Minton, Clive
Moult in birds is a critical yet often underrated component of a birds' annual life cycle together with breeding and migration. A good understanding of the moult strategy of a species is important for its conservation because key moulting grounds must be protected to allow this component of the life cycle to be undertaken. Lesser Sand Plovers, Greater Sand Plovers and Terek Sandpipers are among the least known of the commonly encountered long-distance migrant waders in Africa and Australasia. This is particularly true for the populations which spend the non-breeding season on the East African coast. This study aims to describe the primary moult strategies for the three species from five locations at different latitudes: south-eastern India, Kenya, South Africa, north-western Australia and southeastern Australia. Differences in moult strategy between species, age and latitude are highlighted and explanations are proposed for the differences in the light of the breeding behaviour, migration time and routes, food availability and local climatic conditions. Results from this study are combined with other moult studies on migrant waders to present hitherto undescribed patterns in wader moult strategies at a global scale. A synthesis is presented of published and available unpublished information about the different populations for the three study species, their distribution, status and migration strategies with a focus on those visiting the East African coast. The three species follow a similar basic moult strategy in adults where primaries are moulted soon after arriving on the non-breeding grounds. Immature moult strategies are more complex and differ between species and latitude. In general adults in all three species at the more northern nonbreeding sites start moult earlier than those travelling farther south probably as a result of greater proximity to breeding grounds. Lesser Sand Plovers have a relatively long duration of moult (152- 154 days) across all locations where data were sufficient; Greater Sand Plovers have a short duration (80 days) in India and similar, comparatively longer durations (132-134 days) at the other latitudes. The Indian site is used mainly by this species as a site to stopover and moult while on migration to more southerly non-breeding grounds. Terek Sandpipers in Kenya have a relatively short duration of moult (99 days) when compared to India and Australia (121-130 days) and tend to have a rapid start to moult which then slows down after the first few primaries are moulted. Young Lesser Sand Plovers in India mostly undergo a complete primary moult while in Kenya and Australia birds generally do not moult in their first year. First year Greater Sand Plovers mostly all undergo a complete primary moult irrespective of latitude. Terek Sandpipers in their first year do not moult in India in the north, mostly undergo a partial moult of outer primaries in Kenya on the equator, and do a complete moult in south-eastern Australia. The north-west Australian population was divided into two almost equal groups: those that undergo a complete primary moult, and those that only moult a few outer primaries. A difference in winglength between these two groups suggests that there may be two distinct populations involved, most likely originating from distinct breeding grounds. In-depth study is needed to confirm this. The overarching picture of moult in adult migrant waders is that at high latitudes moult starts early and is kept short. With decreasing latitude, the timing of moult is delayed with increasing distance from breeding grounds. In the tropics the lack of constraints of approaching harsh winter weather and long distances from breeding grounds allow species to adapt a wide range of moult strategies. As birds migrate farther south before they moult, constraints on time available to moult due to large distances travelled mean duration is reduced in order to fit it in. An upper limit in duration of moult in migrant waders irrespective of the size of the bird appears to be set at c. 160 days. Small birds have a wide variation in duration while as body size increases over 100 g, moult duration is necessarily longer. With harsh winters in the north, large waders are forced to migrate south in order to moult. This study suggests that irrespective of body size the 'gold standard' for duration of moult is around 120 days (four months). While timing of migration is relatively well-known for the three species in Australia, it was hitherto unknown that juvenile Lesser Sand Plovers delay in reaching Australia until February or March in contrast to all other migrant wader species where first years arrive in September/October. It is unknown where they stop en route or indeed why they delay in this way. All three species in Kenya peak at a maximum population in November and early December after which numbers reduce as birds start to depart for the breeding grounds. Resightings of colour-flagged Lesser and Greater Sand Plovers confirmed the north-western coast of India as an important stopover site for migrants heading to western China and Mongolian breeding grounds from Kenya. A review of country population estimates for the three species suggested non-breeding populations in Africa of 200,000 Lesser Sand Plovers, 25,000-35,000 Greater Sand Plovers and 115,000-200,000 Terek Sandpipers. Mida Creek is shown to be a key stronghold for non-breeding waders in Kenya and its importance for their continued conservation is thus confirmed.
Open Access
Regional CO₂ flux estimates for South Africa through inverse modelling
(2018) Nickless, Alecia; Rayner, Peter; Scholes, Bob; Erni, Birgit; Underhill, Leslie G
Bayesian inverse modelling provides a top-down technique of verifying emissions and uptake of carbon dioxide (CO₂) from both natural and anthropogenic sources. It relies on accurate measurements of CO₂ concentrations at appropriately placed sites and "best-guess" initial estimates of the biogenic and anthropogenic emissions, together with uncertainty estimates. The Bayesian framework improves current estimates of CO₂ fluxes based on independent measurements of CO₂ concentrations while being constrained by the initial estimates of these fluxes. Monitoring, reporting and verification (MRV) is critical for establishing whether emission reducing activities to mitigate the effects of climate change are being effective, and the Bayesian inverse modelling approach of correcting CO₂ flux estimates provides one of the tools regulators and researchers can use to refine these emission estimates. South Africa is known to be the largest emitter of CO₂ on the African continent. The first major objective of this research project was to carry out such an optimal network design for South Africa. This study used fossil fuel emission estimates from a satellite product based on observations of night-time lights and locations of power stations (Fossil Fuel Data Assimilations System (FFDAS)), and biogenic productivity estimates from a carbon assessment carried out for South Africa to provide the initial CO₂ flux estimates and their uncertainties. Sensitivity analyses considered changes to the covariance matrix and spatial scale of the inversion, as well as different optimisation algorithms, to assess the impact of these specifications on the optimal network solution. This question was addressed in Chapters 2 and 3. The second major objective of this project was to use the Bayesian inverse modelling approach to obtain estimates of CO₂ fluxes over Cape Town and surrounding area. I collected measurements of atmospheric CO₂ concentrations from March 2012 until July 2013 at Robben Island and Hangklip lighthouses. CABLE (Community Atmosphere Biosphere Land Exchange), a land-atmosphere exchange model, provided the biogenic estimates of CO₂ fluxes and their uncertainties. Fossil fuel estimates and uncertainties were obtained by means of an inventory analysis for Cape Town. As an inventory analysis was not available for Cape Town, this exercise formed an additional objective of the project, presented in Chapter 4. A spatially and temporally explicit, high resolution surface of fossil fuel emission estimates was derived from road vehicle, aviation and shipping vessel count data, population census data, and industrial fuel use statistics, making use of well-established emission factors. The city-scale inversion for Cape Town solved for weekly fluxes of CO₂ emissions on a 1 km × 1 km grid, keeping fossil fuel and biogenic emissions as separate sources. I present these results for the Cape Town inversion under the proposed best available configuration of the Bayesian inversion framework in Chapter 5. Due to the large number of CO₂ sources at this spatial and temporal resolution, the reference inversion solved for weekly fluxes in blocks of four weeks at a time. As the uncertainties around the biogenic flux estimates were large, the inversion corrected the prior fluxes predominantly through changes to the biogenic fluxes. I demonstrated the benefit of using a control vector with separate terms for fossil fuel and biogenic flux components. Sensitivity analyses, solving for average weekly fluxes within a monthly inversion, as well as solving for separate weekly fluxes (i.e. solving in one week blocks) were considered. Sensitivity analyses were performed which focused on how changes to the prior information and prior uncertainty estimates and the error correlations of the fluxes would impact on the Bayesian inversion solution. The sensitivity tests are presented in Chapter 6. These sensitivity analyses indicated that refining the estimates of biogenic fluxes and reducing their uncertainties, as well as taking advantage of spatial correlation between areas of homogeneous biota would lead to the greatest improvement in the accuracy and precision of the posterior fluxes from the Cape Town metropolitan area.
Open Access
Secretarybird Sagittarius serpentarius Population Trends and Ecology: Insights from South African Citizen Science Data
(PLoS (Public Library of Science), 2014-05-09) Hofmeyr, Sally D; Symes, Craig T; Underhill, Leslie G
Data from two long-term citizen science projects were used to examine the status and ecology of a Red List species, the Secretarybird Sagittarius serpentarius (Vulnerable), in South Africa. The first phase of the Southern African Bird Atlas Project operated from 1987 until 1992, and the second phase began in 2007. The Coordinated Avifaunal Roadcounts (CAR) project began in 1993 and by 1998 had expanded to cover much of the south-eastern half of the country. Data submitted up until April 2013 were used. A new method of comparing reporting rates between atlas projects was developed. Changing reporting rates are likely to reflect changes in abundance; in this instance the data suggest that the Secretarybird population decreased across much of South Africa between the two atlas projects, with a widespread important decrease in the Kruger National Park. Habitat data from the CAR project were analysed to gain insight into the ecology of the species. Secretarybirds tended to avoid transformed habitats across much of the area covered by the CAR project. In the winter rainfall region of the Western Cape, which is characterised by heavily transformed fynbos vegetation, at least 50% of Secretarybirds recorded were in transformed environments. This implies that in the Fynbos biome, at least, Secretarybirds have adapted to transformed environments to some degree. However, in the rest of the country it is likely that habitat loss, largely through widespread bush encroachment but also through agriculture, afforestation, and urbanisation, is a major threat to the species. The methods developed here represent a new approach to analysing data from long-term citizen science projects, which can provide important insights into a species’ conservation status and ecology.
Open Access
A simulation study of the effect of target motion on sighting estimates of minke whale population density
(1983) Basson, Marinelle; Butterworth, Doug S; Underhill, Leslie G
Line transect methods used to estimate population density assume stationarity of targets. Violation of this assumption leads to overestimation of the true density. A simulation study based on a hazard-rate model is used to assess the resulting bias. The model is calibrated to generate sighting data resembling real data from minke whale sighting surveys. The procedure currently used to calculate a corrected negative exponential density estimate from sighting data is duplicated using simulated data. The resulting estimates are compared to the true population density determined by the simulation. Results reveal that in the case considered, the method of calculating the g(O) factor (which corrects for the fact that all animals on the trackline are not sighted) leads to a greater degree of overestimation than the effect of target motion at 3 knots. Shortcomings of the model are pointed out and possible improvements suggested. It is also suggested that further research be focused initially on the calculation of the g(O) correction factor rather than on effects of target motion.
Open Access
Statistical analysis of bird atlas data from Swaziland
(1995) Parker, Vincent; Underhill, Leslie G
The question of what determines the observed geographical distributions of animal species is one of great interest to natural scientists. In general terms, these distributions are known to be related to a number of environmental factors, but the nature of the relationships and the relative importance of the different factors remain poorly understood. This investigation sets out to obtain more insight into these questions by using statistical methods to explore the relationships between the observed geographical distributions of bird species in Swaziland and a number of environmental variables. In 1985 I set out to compile a bird atlas of Swaziland. Data were accumulated between 1985 and 1991 and the bird atlas submitted to a publisher in May 1993. The text of the bird atlas is included here as Appendix 2 because it provides the essential background to this dissertation. The introductory section of the atlas includes a description of the data gathering process. The analysis included in the bird atlas was aimed at a popular readership and was not intended to form part of an academic dissertation Chapter 1 describes the use of logistic regression to investigate the relationships between the bird distribution patterns and a set of environmental variables and to predict the distributions. Chapter 2 describes the results of applying the methods described in Chapter 1 for all of the bird species for which data were available. Because this paper was aimed at a different readership, some repetition of material contained in Chapter 1 was unavoidable. In Chapter 3, biplot techniques were used to obtain a graphical representation of the bird atlas data.
Open Access
There might be a frog in McElligot's Pool: a study of the habitat characteristics and social factors associated with amphibian presence in urban residential gardens in a suburb in Cape Town
(2017) Brom, Peta; Anderson, Pippin; Underhill, Leslie G; Channing, Alan
This thesis engages with urban ecology through the lens of garden amphibians within a community in Cape Town. The study explores habitat and maintenance features associated with amphibian presence and the social processes underpinning attitudes towards amphibians, with the aim of strengthening knowledge underpinning the "what" (knowledge of natural requirements), "Why" (social drivers for urban landscape form and management), and the "how" (working with people, for garden biodiversity initiatives. To explore the "Why" component, a social survey was conducted with 192 members of the community. One‐way anova and correspondence analysis were used to explore the relationship between values, culture, knowledge and memories of early childhood experiences against a general attitude towards frogs and toads. The findings are consistent with the theoretical framework of Connectedness To Nature where positive attitudes are supported by normative values, cultural beliefs, knowledge and positive experiences with care‐givers and role‐models. The garden habitat component of the study sought to explore the technical questions of the "What" requirement for amphibian presence in gardens. It was loosely based on the BIMBY tool with adaptations for context and targeted species. 50 gardens were visited and surveyed. They were divided into two groups for comparison: Those in which residents reported amphibian presence, and those which did not. Results indicate that the cape river frog (A. fuscigula) and clicking stream frog (S. grayii), are attracted to gardens with moderate to dense vegetation at groundcover level. Gardens with moderately planted beds were more likely to report frogs if they had additional resources, in particular, ponds and mulch. The "How" question brought together the two themes in a discussion on citizen mobilization and ways in which community groups are successfully implementing urban ecology conservation and reconciliation strategies. This work is important for urban nature conservation which seeks to engage private land‐owners (garden enthusiasts) and community and citizen groups in implementing urban biodiversity projects.
Open Access
Towards adaptive management of high-altitude grasslands: Ingula as a case study
(2015) Maphisa, David Hlosi; Altwegg, Res; Underhill, Leslie G
Eastern high - altitude grasslands of South Africa are centres for endemism and harbour fauna and flora of regional and international conservation concern. This area also provides important ecological services such as provision of water to communities downstream. Sweet and sour veld support beef livestock farming during summer months. The aesthetic beauty of the region makes the area a prime tourist destination too. More recently the area is becoming a target of other agricultural projects such man - made forests. Other new developments that need to be mitigated against are development of renewable energy projects such as pumped water schemes to generate electricity or wind farms. Additional habitat is lost when these projects are connected to the national grid. In this thesis, I use bird data and vegetation data to compare, contrast and suggest management tools to manage this area. I present data that I collected at Ingula Pumped Storage Scheme spanning five years from the beginning of the construction of the scheme to near its completion in 2012 as a case study to manage similar habitats. Chapter 1 presents a brief overview of ecological importance of this area and the history behind the construction of pumped storage scheme at Ingula. A literature review in Chapter 2 investigates management tools to manage these grasslands for avian diversity. Fire and grazing is a key management tool cited to make habitat suitable for birds. While few studies from this type of grassland exist, studies from outside South Africa suggest that fire and grazing supplement each other as management tool to make habitat suitable for species with contrasting ecological requirements. A mosaic of grass heights and cover across the landscape translates to species habitat suitability. Chapter 3 explores species richness through years, seasons and impact of grass height and cover on bird species richness. Species richness was highest in summer suggesting that management should make habitat for species suitable in summer when most priority species are likely to use the habitat. The main disadvantage of using bird species richness is that fieldworkers must know their species well. Secondly, use of species richness must be treated with caution because this method does not account for species detectability in time and in space. In Chapter 4 I use hierarchical distance sampling models which take into account both the detection and the biological process. To demonstrate this I used common grassland bird species which can easily be identified during monitoring. The downside of this approach is that because these species are common and therefore occur almost everywhere, they may not easily respond to lack of habitat heterogeneity. The technical disadvantage of using this method is to accurately allocate species to within distance bands, making this method challenging for fieldworkers. Chapter 5 presents random plot occupancy which records only detection - nondetection of birds during repeated plot surveys. This method accounts for observational and biological processes too and in addition implements rigorous statistical inferences to predict how birds respond to habitat variable s as influenced by management decision on fire and grazing. Finally, adverse weather conditions may hamper surveying all plots in some years. Through occupancy modelling it is possible to predict species occupancy on plots that were not surveyed during some years and finally this method has been improved to include rare species. This is my preferred method to monitor management effect on habitat suitability for birds at Ingula. Adaptive management, a pillar of which is adaptive monitoring is a new paradigm shift in conservation. In Chapter 6, I capture interactions between burning and grazing and effects on grass height and cover to predict habitat suitability for birds including large threatened Ingula birds using a simulation models. This model sets a stage for implementing adaptive management through experimental plots to capture a set of management uncertainties regarding the use of fire and grazing as management tools. Chapter 7 summarizes the thesis and acknowledges that Ingula consists of other equally important habitat and ecosystem such as cool moist mountain forest and matrix of grassland wetland that equally need to be conserved.

Browsing by Author "Underhill, Leslie G"

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