Thesis (MSc (Conservation Ecology and Entomology)--Stellenbosch University, 2007. / A systematic conservation assessment is the first phase of a systematic conservation planning protocol; it uses spatial data and representation targets for the setting of priority areas and the assessment of risk to biodiversity. This thesis describes the findings of investigations on the use of data in systematic conservation assessments. Conservation planning can be done at different spatial scales (from global to local). Systematic Conservation planning can be done at different spatial scales (from global to local). Systematic conservation assessments rely on the use of surrogates for biodiversity and often, as well, socioeconomic criteria. Biodiversity surrogates can be classified as taxonomic, community and environmental. In Chapter 2, a literature review was performed (i) to quantify the use of biodiversity surrogates and socio-economic criteria in conservation assessments; and (ii) to test the hypothesis that surrogates are chosen in respect to the hierarchical organisation of biodiversity. In other words, fine scale conservation assessments are correlated with taxonomic surrogates, large scale conservation assessments are correlated with environmental surrogates, and assemblage surrogates are assessed at an intermediary scale. The literature review was based on a structured survey of 100 ISI journal publications. The analysis revealed that spatial scale had a weak effect on the use of biodiversity surrogates in conservation assessments. Taxonomic surrogates were the most used biodiversity surrogates at all scales. Socioeconomic criteria were used in many conservation assessments. I argue that it is crucial that assemblage and environmental data be more used at larger spatial scales. The allocation of conservation resources needs to be optimised because resources are scarce. A conservation assessment can be a lengthy and expensive process, especially when conducted at finescale. Therefore the need to undertake a fine-scale conservation assessment, as opposed to a more rapid and less expensive broader one, should be carefully considered. The study of Chapter 3 assessed the complementarity between regional- and local-scale assessments and the implications on the choice of biodiversity features at both scales. The study was undertaken in Réunion Island. A biodiversity assessment was performed at a regional scale and measured against a finer-scale assessment performed over a smaller planning domain. Two datasets composed of species distributions, habitat patterns and spatial components of ecological and evolutionary processes were compiled as biodiversity surrogates at each scale. Targets for local-scale processes were never met in regional assessments, while threatened species and fragmented habitats were also usually missed. The regional assessment targeting habitats represented a high proportion of local-scale species and habitats at target level (67%). On the contrary, the one targeting species was the least effective. The results highlighted that all three types of surrogates are necessary. They further suggested (i) that a spatial strategy based on a complementary set of coarse filters for regional-scale assessments and fine filters for local-scale ones can be an effective approach to systematic conservation assessments; and (ii) that information on habitat transformation should help identify where efforts should be focused for the fine-scale mapping of fine filters. Together with priority-area setting, the identification of threatened biodiversity features has helped to prioritise conservation resources. In recent years, this type of assessment has been applied more widely at ecosystem-level. Ecosystems can be categorised into critically endangered, endangered and vulnerable, following the terminology of the IUCN Red List of threatened species. Various criteria such as extent and rate of habitat loss, species diversity and habitat fragmentation can be used to identify threatened ecosystems. An approach based only on the criterion of the quantification of habitat loss was investigated in Chapter 4 for the Little Karoo, South Africa. Habitat loss within ecosystem type is quantified on land cover information. The study analysed the sensitivity of the categorisation process to ecosystem and land cover mapping, using different datasets of each. Three ecosystem classifications and three land cover maps, of different spatial resolutions, were used to produce nine assessments. The results of these assessments were inconsistent. The quantification of habitat loss varied across land cover databases due to differences in their mapping accuracy. It was reflected on the identification of threatened ecosystems of all three ecosystem classifications. Less than 14% of extant areas were classified threatened with the coarsest land cover maps, in comparison to 30% with the finest one; and less than 9% of ecosystem types were threatened with the coarsest land cover maps, but between 15 and 23% were threatened with the finest one. Furthermore, the results suggested that the identification of threatened ecosystems is more sensitive to the accuracy of habitat loss quantification than the resolution of the ecosystem classification. Detailed land cover mapping should be prioritised over detailed ecosystem maps for this exercise. This thesis highlighted the importance of ecosystems and processes as biodiversity surrogates in conservation assessments and suggested that results of conservation assessments based on these data, should be more widely presented in published articles. Finally, it also made apparent the important role of mapping habitat transformation for systematic conservation plans.