Future-proofing conservation: applying systematic conservation planning to prevent extinction under climate and land use change

Humans have been reshaping the environment of Earth for thousands of years. However, the intensity of anthropogenic pressures has rapidly increased in recent decades, pushing an evergreater number of species towards extinction. The primary driver of modern extinctions is habitat loss, while climate change is projected to become the leading cause of biodiversity loss in the future. To mitigate these impacts and reverse these trends, nations have committed to halt the extinction of threatened species by mid-century, and to protect 30% of global land and sea by 2030 (known as the ‘30 by 30’ target). There is now an urgent need to understand how such targets can be achieved in a way that is deliverable, effective, and resilient to future climate and land use change. To answer this question, my thesis considers how systematic conservation planning approaches can optimise conservation interventions both in situ (such as protected area planning) and ex situ (such as conservation of threatened species in zoos). I show that both existing protected areas and current zoo collections must evolve significantly if they are to avoid being outpaced by anthropogenic environmental change. First, I model the impact of climate change on most of the world’s terrestrial vertebrate species (n = 24,598), and identify spatial and phylogenetic shifts in the distribution of threatened biodiversity globally. Using these data, I highlight spatial priorities for area-based conservation, achieving 30 by 30 in a manner that maximises the long-term conservation of threatened evolutionary history under environmental change. I then turn to ex situ conservation in zoos, finding that collections must adapt significantly if they are to conserve the taxa most threatened by climate and land use change. As zoos must house appealing species that drive visitation rates, I then investigate the traits that underpin species attractiveness to zoo visitors, with highly active, visible mammals proving the most attractive. I use these results to highlight opportunities to leverage species appeal and maximise investment in conservation. Finally, I bring this information together and apply, for the first time, conservation optimisation algorithms to zoo collection planning at global and regional scales. Such approaches can increase the protection of threatened evolutionary history by approximately an order of magnitude, both in situ and ex situ, relative to existing protected areas and zoo collections, respectively. These results pose both a challenge and an opportunity to the conservation community, highlighting both the scale of adaptation required, but also the huge potential conservation benefits that could be achieved, even as anthropogenic climate and land use change intensify

Ecotourism and its ecological impact: A study of tourist developments in the Mara

The increased growth of wildlife tourism in Kenya over the last few decades has placed increasing demand and attention for the development and subsequent delivery of sustainable tourism. Today ecotourism ventures are perceived by many as a solution to the negative impacts of "traditional" wildlife tourism and thus a way to achieve ecologicalsustainability within the industry. To date however, there has been no attempt to qualifyand quantify any possible wildlife impacts of ecotourism - the basis of this research, usingthe Mara Ecosystem as a case study. Using WildKnowledge© software, this research recorded biotic and abiotic data from wildlife tourism developments of various sizes and assessed their anthropogenic impacts upon key ungulate species in the ecosystem over a three year period. The findings of this aspect of the research indicate that the effects of the tourism industry on wildlife are highly species specific. In particular Buffalo were most affected by differences in tourism seasonal variability (X2=5.040, df=l, p=O.025), distance to developments (X2=23.341, df=l, p=O.OOO) and group size (X2=7.998, df=1, p=O.005) between the different lodge types. In contrast, waterbuck and eland displayed similar patterns of disturbance irrespective of lodge type or tourism seasonal variability. Using historical species count data spanning a twenty year period, kernel density maps were constructed to demonstrate spatial changes in ungulate density and distribution patterns in relation to tourism growth. The resulting density maps revealed that while the national reserve offered a measure of security to wildlife, many ungulate species still heavily utilised their historical dispersal areas in the community lands. Interestingly, despite the tourism related land use changes demonstrated in the Mara's landscape, some species e.g. eland, displayed an increase in range size - to 4s0.5km2 in 2010 from 399.Skm2 in 2005 following the creation of wildlife conservancies in the surrounding ranches.Constructing site suitability models, the research explored how GIS modelling techniques can be employed to identify suitable locations for tourist accommodation, without compromising the ecological integrity of the wildlife areas where these facilities will be located. Employing two different bed occupancy models (conservancy model; 350 acres/bed and a current model; ; 174 acres/bed, derived from existing facilities), the Mara Ecosystem's ability to accommodate further tourism growth at low ecological cost was demonstrated. Application of the highest suitability criteria to select potential development sites revealed two suitable locations. A further 54 locations were identified as suitable for ecocamps and ecolodges on application of the second highest site selection suitability criteria. Importantly, the models employed clearly demonstrate that the majority of future ecotourism facilities be located outside the National Reserve in the group ranches if they are to have limited wildlife impact, as over-utilisation of any single sections of the ecosystem will lead to resource depletion and localized species loss. The results presented highlight the need for a more integrative approach to ecotourism provision. The utility of GIS based models to project the impacts of human disturbances on wildlife populations under different tourism scenarios is reinforced by this research. These suitability models are easily modified and can therefore be used under different planning scenarios in other wildlife areas in Kenya and the region. It is therefore hoped, that the results from this study will influence policy direction for tourism planning in wildlife areas for the Mara and other ecosystems, and be used to complement the country's tourism and wildlife bills which are about to be passed into law. This research concludes that although ecotourism plays an important role in environmental conservation, its ecological impacts on wildlife in receiving environments can be significant and should be a primary consideration in deciding upon the efficacy of individual proposals

Effects of urban expansion on coastal vegetation ecosystems conservation and functioning in Buffalo City Metropolitan Municipality, South Africa

Coastal urban expansion is on an upward trajectory, which poses serious threats to ecosystem functioning, human wellbeing and the general environment across the globe. It is on this premise that this study brings to the fore the growing complexity of environmental sustainability problems in a former apartheid space, as characterized by coastal urbanization and the intricacies of vegetation conservation. Consequently, literature utilized for this study reveals that urban expansion has led to an uncontrolled threat to the coastal ecosystem, culminating in soil erosion, environmental pollution through illegal dumping of solid waste, loss of coastal vegetation to other land use types, among others. Therefore, constant monitoring of these spaces is needed due to their fragility, as they are pivotal in the earth-atmosphere processes to the benefit of the entire humanity. To this end, the current study offers critical analysis and insights about the South African coastal ecological space. The essence of using BCMM in its consideration as an ecological space and former apartheid territory brings to the fore a scientific explanation of the spatial configuration and changes in the CVEs of the study area during the post-colonial era. In the course of investigating this study, the Urban Green Sustainability (UGS) theory was adopted in the course of selecting the review of literature, methodological approach and analysis of results. A mixed methodological approach (qualitative, quantitative and geospatial techniques) was explored in data collection and analysis. 254 copies of the questionnaire were returned and analysed for this research. Results generated revealed by the BCMM respondents confirms the occurrence of uncontrolled urbanization, deforestation and crop cultivation as major causes of coastal vegetation loss. In the same vein, the LULC classification results revealed that about 466 km2 of forest vegetation has been lost in BCMM from 1998-2018. Also, LULC classification results were validated by performing the Normalized Difference Built-Up Index (NDBI), Normalized Difference Vegetative Index (NDVI), Kappa’s coefficient (k), coefficient of determination (R2) and Pearson’s Product Moment Correlation (P) tests. The results also revealed that the built-up area had increased from 194 km2 in 1998 to 814 km2 in 2008. Further, all statistical tests revealed very good and highly correlated overall classification accuracies (of R2=0.89 and P=0.86) during the study period (1998 – 2018). This study makes a clarion call towards the rehabilitation of degraded coastal environments and proffers solutions towards the actualization of environmentally sustainable CVEs which offers optimal ecosystem services.Thesis (PhD) -- Faculty of Science and Agriculture, 202

Effects of urban expansion on coastal vegetation ecosystems conservation and functioning in Buffalo City Metropolitan Municipality, South Africa

Coastal urban expansion is on an upward trajectory, which poses serious threats to ecosystem functioning, human wellbeing and the general environment across the globe. It is on this premise that this study brings to the fore the growing complexity of environmental sustainability problems in a former apartheid space, as characterized by coastal urbanization and the intricacies of vegetation conservation. Consequently, literature utilized for this study reveals that urban expansion has led to an uncontrolled threat to the coastal ecosystem, culminating in soil erosion, environmental pollution through illegal dumping of solid waste, loss of coastal vegetation to other land use types, among others. Therefore, constant monitoring of these spaces is needed due to their fragility, as they are pivotal in the earth-atmosphere processes to the benefit of the entire humanity. To this end, the current study offers critical analysis and insights about the South African coastal ecological space. The essence of using BCMM in its consideration as an ecological space and former apartheid territory brings to the fore a scientific explanation of the spatial configuration and changes in the CVEs of the study area during the post-colonial era. In the course of investigating this study, the Urban Green Sustainability (UGS) theory was adopted in the course of selecting the review of literature, methodological approach and analysis of results. A mixed methodological approach (qualitative, quantitative and geospatial techniques) was explored in data collection and analysis. 254 copies of the questionnaire were returned and analysed for this research. Results generated revealed by the BCMM respondents confirms the occurrence of uncontrolled urbanization, deforestation and crop cultivation as major causes of coastal vegetation loss. In the same vein, the LULC classification results revealed that about 466 km2 of forest vegetation has been lost in BCMM from 1998-2018. Also, LULC classification results were validated by performing the Normalized Difference Built-Up Index (NDBI), Normalized Difference Vegetative Index (NDVI), Kappa’s coefficient (k), coefficient of determination (R2) and Pearson’s Product Moment Correlation (P) tests. The results also revealed that the built-up area had increased from 194 km2 in 1998 to 814 km2 in 2008. Further, all statistical tests revealed very good and highly correlated overall classification accuracies (of R2=0.89 and P=0.86) during the study period (1998 – 2018). This study makes a clarion call towards the rehabilitation of degraded coastal environments and proffers solutions towards the actualization of environmentally sustainable CVEs which offers optimal ecosystem services.Thesis (PhD) -- Faculty of Science and Agriculture, 202

Incorporating costs and processes into systematic conservation planning in a biodiversity hotspot

Given inadequate budgets with which to stem the rapid destruction of biodiversity, conservationists must set clear priorities for action. Systematic Conservation Planning (SCP) is an approach that uses spatially explicit data to identify areas that meet conservation targets efficiently, usually focusing on species’ representation. Only rarely is the long-term persistence of species taken into account and the costs of conservation are usually ignored. I use the Eastern Arc Mountains of Tanzania as a study area to develop novel methods for creating and integrating the necessary data to fill these gaps in a developing country context. These mountains exhibit exceptional biodiversity but are also highly imperilled. I describe the biological data that I assembled for use in a series of SCP analyses. Fine-scale distribution models for species were mapped for over 500 animal and plant species of conservation concern. I then mapped Ecological and Evolutionary Processes (EEPs), which are crucial to species’ persistence and contribute to healthy ecosystem functioning. My analyses show how the inclusion of biological processes can significantly alter priorities when compared to prioritisation using information on species’ presence alone. Despite their importance, EEPs are often excluded from SCP. This is largely due to the difficulties involved in expressing them quantitatively and in optimising reserve networks to represent them at a minimum cost. This reluctance should be challenged, otherwise reserve networks will, over time, lose those elements of biodiversity that they were established to conserve. I also investigate conservation costs. Despite chronic underfunding for conservation and the recognition that funds must be invested wisely, few data on the costs of conservation are available at the spatial scales needed to inform local site management. I present methods for estimating and mapping protected area management costs, wildlife damage cost and the opportunity costs of conservation. Costs are highest in densely populated and cultivated areas, particularly in the north, whereas large areas of the more remote mountain blocs in the south show lower costs. Integrating these data into SCP demonstrates that using real cost data (rather than assuming that cost per unit area is homogenous) alters priorities and increases the efficiency of conservation within the Eastern Arc. Importantly, the efficiency savings realised through using cost, rather than area, to prioritise conservation efforts were found to be most pronounced when budgets were limited so that not all conservation targets could be met

From space to species: integrating remotely sensed information on primary productivity into investigations and systems models of vervet monkey (Cercopithecus aethiops) socio ecology

An in depth investigation of the socio-ecology of the vervet monkey species complex (Cercopithecus aethiops subspp.) is presented. Herein, particular emphasis has been placed on evaluating the information content of remotely sensed primary productivity with respect to inquiries into the causal network underlying the behavioural ecology of the species. The principal aim was to construct an inter-populational model of group size and range of distribution for vervet monkeys over the whole of sub-Saharan Africa. Data were collected on a habituated group of vervet monkeys over a 12 months observation period at the Lajuma Research Centre, South Africa. In addition, behavioural information from other populations was gathered in an extensive literature review. Environmental data were accrued on both a global (inter-populational) and local (intra- populational) level using a combination of remotely sensed data and more traditional field-observation based techniques. Where appropriate, variables were integrated into the powerful modelling environment of a Geographical Information System (GIS).Biologically intuitive associations between a remotely sensed index of primary productivity (the Normalised Difference Vegetation Index, or NDVI) and climatic conditions were established on the long-term global (annual average values over sub- Saharan Africa) and short-term local level (monthly values over the home range area of the study group). Local NDVI values, moreover, were strong correlates and predictors of field estimates on local phenology and food availability as well as of temporal and spatial variation in parameters of range use and time allocation by the study group. Global NDVI values proved pivotal to the eventual inter-populational time budget model of vervet monkey group size and potential range of distribution. Current results are taken to suggest that several areas of research within primatology may stand a lot to gain from a more widespread and systematic application of the powerful methodological synergism offered by remote sensing and geographical information systems

Multi-attribute value measurement and economic paradigms in environmental decision making

Bibliography: p. 219-228.The two environmental decision-making approaches of environmental economics (EE) valuation and multi-criteria decision analysis (MCDA) differ fundamentally in their underlying philosophies and approach; hence they are characterised as paradigms. The EE paradigm includes the idea that, if appropriate prices can be found and implemented for goods not normally traded on the market, then the market mechanism will efficiently distribute resources and decisions are therefore based on the concepts of individual willingness to pay and consumer sovereignty. That an efficient market is not necessarily equitable or sustainable has long been acknowledged, but EE adjustments are subject to theoretical and methodological problems. The MCDA paradigm is based on the idea that values and preferences should be examined and constructed through interaction between workshop participants and the analyst, given basic measurement theory axioms. Various EE and MCDA methods have been devised for measuring value in different contexts, some of which were applied, in the context of environmental (particularly water resources) management, in six action research case studies. The EE methods were contingent behaviour valuation, the contingent valuation method, conjoint analysis and the travel cost method. The MCDA method was a version of the simple multi-attribute rating technique (called SMARTx). In the SMARTx cases, applying a group-value sharing model during a series of workshops, stakeholders rated the effect of alternatives on a number of environmental, social and economic attributes directly or using value functions and gave weights to criteria. Indirect compensatory values of one criterion in terms of another were determined. In the EE cases, survey respondents were asked their travel costs, preference for multi-attribute profiles and willingness to pay for alternatives. Total and average willingness to pay for an amenity, its attributes or changes in environmental quality were determined. The practical and theoretical implications of applying the different methods were examined and compared in terms of four metacriteria: resonance with and validity within the prevailing political and decision-context, general validity and reliability, ability to include equity and sustainability criteria and practicality

The molecular and genetic evolution of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) (Family: Picornaviridae, Genus: Aphthovirus) is a significant global pathogen with extensive economic impact. FMDV has a low fidelity RNA-dependent RNA polymerase and lacks proof reading capability. This coupled with its relatively short generation time and large population sizes means it exists in a swarm of genetically closely related variants. The reservoir of diversity contained within this mutant spectrum allows the virus to adapt rapidly to new environments. Much of the previous work looking at virus evolution has focused on the consensus level genetic sequence. The advent of next generation sequencing (NGS) technologies enables evolutionary studies of the entire viral swarm. This PhD project uses NGS technologies to interrogate the swarm structure by investigating factors affecting the viral swarm and the dynamics of variants within it. Furthermore, this work shows how analysis of the swarm can reveal fundamental information about virus biology. A PCR-free NGS methodology was developed to create deep sequencing data sets of all genomes present within an FMDV viral swarm. The elimination of the PCR step results in less errors being introduced in the sequencing process thereby improving the resolution and reliability of the identification of low level variants. This optimised method was then used to define and compare the FMDV swarms of several wildtype isolates. This revealed differences in swarm structure from isolate to isolate and produced evidence of within swarm selection. Not all proteins known to be under selection at the consensus level were also under selection within the swarm. The diversity of viruses within the swarm was found to be dependent upon the host from which a virus was sampled, with African buffalo potentially able to maintain multiple infections. Subconsensus variants in these mixed samples had mutations at positions previously associated with immune escape. Investigation of the evolution of swarm structure when adapting to new cell type in vitro indicated that two distinct population structures can exist relative to the existence of adaptive pressure. These two population structures have different distributions of variable nucleotides but comparative total levels of variation (as measured by Shannon's entropy). Deep sequencing of the virus swarm enabled the discovery of conserved novel stem loop structures, which were hypothesized to be required for packaging of the virus genome. Mutating these sites produced a virus with decreased packaging efficiency. This thesis includes novel analysis techniques for considering the viral swarm. It demonstrates how investigating the diversity in the swarm can help us to understand virus molecular biology, its evolution and the limits upon this. Understanding viral evolution at this scale has the capacity to improve our fundamental understanding of the biology and evolution of FMDV which can in turn inform vaccine design and disease control strategie