The Cape Peninsula, South Africa: physiographical, biological and historical background to an extraordinary hot-spot of biodiversity

The Cape Peninsula, a 470 km² area of rugged scenery and varied climate, is located at the southwestern tip of the Cape Floristic Region, South Africa. The Peninsula is home to 2285 plant species and is a globally important hot-spot of biodiversity for higher plants and invertebrates. This paper provides a broad overview of the physiography, biological attributes and history of human occupation of the Peninsula. The Peninsula is characterized physiographically by extremely high topographical heterogeneity, very long and steep gradients in annual rainfall, and a great diversity of nutrient-poor soils. Thus, the Peninsula supports a high number of habitats and ecological communities. The predominant vegetation is fynbos, a fire-prone shrubland, and 12 broadly characterized fynbos types have been described on the Peninsula. Animal community structure, especially with regard to invertebrates, is poorly known. Vertebrate community structure is probably strongly influenced by nutrient poverty and recurrent fire. Generally, most vertebrates are small and typically occur in low numbers. Some invertebrates play keystone roles in facilitating ecological processes. Human occupation of the Peninsula was limited, until relatively recently, by nutrient poverty. After Dutch colonization in 1652, direct and indirect impacts on the natural ecosystems of the Peninsula escalated dramatically, and by 1994, some 65% of original natural habitat was either transformed by urbanization and agriculture, or invaded by alien plants. Nonetheless, there is still excellent potential to conserve the Cape Peninsula's remaining biodiversity.     

New species and combinations in the African Restionaceae

Eight new species of the African Restionaceae (Restionoideae) are described, viz.: Cannomois anfracta, Cannomois arenicola, Cannomois grandis, Nevillea vlokii, Thamnochortus kammanassiae, Willdenowia pilleata, Restio uniflorus and Restio mkambatiae. A key to the species of Cannomois is provided, as well as a table comparing the characters of the three species in Nevillea. For all new species, notes on the affinities of the species and their habitats are provided. Two new combinations, Cannomois primosii (Pillans) H.P. Linder and Cannomois robusta (Kunth) H.P. Linder, are made.     

Biogeographic patterns and phylogeography of dwarf chameleons (Bradypodion) in an African biodiversity hotspot

The southern African landscape appears to have experienced frequent shifts in vegetation associated with climatic change through the mid-Miocene and Plio-Pleistocene. One group whose historical biogeography may have been affected by these fluctuations are the dwarf chameleons (Bradypodion), due to their associations with distinct vegetation types. Thus, this group provides an opportunity to investigate historical biogeography in light of climatic fluctuations. A total of 138 dwarf chameleons from the Cape Floristic Region of South Africa were sequenced for two mitochondrial genes (ND2 and 16S), and resulting phylogenetic analyses showed two well-supported clades that are distributed allopatrically. Within clades, diversity among some lineages was low, and haplotype networks showed patterns of reticulate evolution and incomplete lineage sorting, suggesting relatively recent origins for some of these lineages. A dispersal-vicariance analysis and a relaxed Bayesian clock suggest that vicariance between the two main clades occurred in the mid-Miocene, and that both dispersal and vicariance have played a role in shaping present-day distributions. These analyses also suggest that the most recent series of lineage diversification events probably occurred within the last 3-6 million years. This suggests that the origins of many present-day lineages were founded in the Plio-Pleistocene, a time period that corresponds to the reduction of forests in the region and the establishment of the fynbos biome.     

Patterns of endemism in the limestone flora of South African lowland fynbos

Taxonomie and biological aspects of endemism and Red Data Book status were studied amongst the limestone endemics of the lowland fynbos in the Cape Floristic Region, South Africa. Of the 110 limestone endemics, 1.8% are widely distributed in the Cape Floristic Region and 56.4% are regional endemics. Relative to flora of non-limestone lowland fynbos (n=538 species), the families which were overrepresented in terms of limestone endemics included the Ericaceae, Fabaceae, Polygalaceae, Rutaceae and Sterculiaceae. The Restionaceae was the only underrepresented family. The local limestone endemics were not significantly different from regional endemics in terms of their biological attributes. An analysis of the frequency of the biological traits associated with the limestone-endemic flora established a biological profile for a limestone endemic: a dwarf-to-low shrub with soil-stored seeds which are ant or wind dispersed. In terms of the species richness of limestone endemics, the De Hoop Nature Reserve was the hotspot within the region. Relative to the total species richness, the Hagelkraal and Stilbaai areas contained higher-than-predicted numbers of rare species. These areas require urgent attention if the unique floral diversity associated with limestone substrata within the Bredasdorp-Riversdale centre of endemism is to be conserved.     

Endemism and speciation in a lowland flora from the Gape Floristic Region

Taxonomic, edaphic and biological aspects of endemism were studied in a phanerogamous flora from the Agulhas Plain, a coastal lowland area of the Cape Floristic Region. Of the 1751 species in the flora, 23.6% were regional endemics and 5.7% were local endemics. Families which were over-represented in terms of endemics included the Ericaceae, Rutaceae, Proteaceae and Polygalaceae. Under-represented families included the Poaceae, Cyperaceae, Scrophulariaceae and Orchidaceae. Highest levels of local endemism were recorded on limestone and colluvial acid sand. Sixty-nine percent of regional endemics and 85% of local endemics were confined to a single substratum. An analysis of the frequency of biological traits associated with species with different categories of endemism enabled the establishment of a biological profile of a local endemic: a dwarf to low, non-sprouting shrub with soil stored seeds which are ant-dispersed and/or form a symbiotic relationship with microbes. It is argued that lineages with these characteristics are vulnerable to severe population reduction or even local extinction. An effect of this would be the promotion of rapid, edaphic speciation as a result of catastrophic selection. Thus, certain traits (e.g. non-sprouting) prevail or even predominate in the flora not because of any adaptive advantage but because high speciation rates of lineages which possess them, overwhelm low survival rates.     

What can phylogenetics tell us about speciation in the Cape flora?

The spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so-called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non-Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.     

Current and future threats to plant biodiversity on the Cape Peninsula, South Africa

The biodiversity of the Cape Peninsula (49127 ha in extent) has been considerably affected by various factors since European settlement in 1652. Urbanization and agriculture have transformed 37% of the original area of natural vegetation. Lowland vegetation types have been worst affected, with almost half of the transformation occurring in one of the 15 recognized vegetation types. Vegetation at high altitudes has been little affected by urbanization and agriculture, but alien trees and shrubs are now threatening biodiversity in these areas. Of the area not affected by urbanization and agriculture 10.7% is currently under dense stands (>25% canopy cover) of alien plants and another 32.9% is lightly invaded. Dense stands of Acacia cyclops, the most widespread invader, cover 2510 ha, 76% of the total area under dense alien stands. This paper assesses the impacts of these factors on aspects of the plant biodiversity of the area, namely, the distribution of major vegetation types and of endemic, rare and threatened plant taxa and of taxa in the Proteaceae (a prominent element in almost all communities, taken as an indicator of overall plant biodiversity).Possible future impacts on biodiversity are assessed by considering the effects of several scenarios involving increased urbanization and changes to alien plant control strategies and further spread over the next 50–100 years. The worst-case scenario for urbanization sees the area under natural vegelation reduced to 12163 ha (39.3% of its extent in 1994, or 24.8% of its original extent). Under this scenario almost a quater of the 161 endemic, rare and threatened (special) taxa are confined totally to urban areas; 57.4% of the known localities of these taxa, and 40.1% of the remaining localities of Proteaceae taxa are transformed. Dense alien stands currently affect 29.8% of the localities of special taxa known from herbarium records and 8.4% of these taxa currently occur only in areas at present affected by aliens. Clearing all dense stands would result in 62.9% of special taxa having less than half of their known localities affected (49.1% at present). Under this scenario, 92% of Proteaceae taxa have more than 75% of their localities unaffected by aliens. If clearing is confined to specific areas (the Cape Peninsula Protected Natural Environment or all publicly-owned land) and the aliens spread further outside these areas, the area of natural vegetation remaining shrinks (to 82.4% of the current extent if control is confined to public land). The further losses in biodiversity associated with these scenarios are described. If control programmes collapse and all potentially invadable land is occupied by dense alien stands, only 407 ha of natural vegetation would remain (1.5% of the current extent).The probability of the various scenarios materializing is discussed. To minimize further losses in biodiversity it is essential that: (1) a major initiative is launched immediately to clear (firstly) the 10184 ha of lightly invaded vegetation and then the 3313 ha of densely invaded vegetation; (2) no urban development be permitted within the boundaries of the Cape Peninsula Protected Natural Environment; (3) a systematic programme of prescribed burning (linked to the alien control programme) is initiated; and (4) contingency measures are implemented to improve the status of seriously threatened taxa, habitats and vegetation types.     

Reconstructing ancestral ecologies: challenges and possible solutions

There are several ways to extract information about the evolutionary ecology of clades from their phylogenies. Of these, character state optimization and 'ancestor reconstruction' are perhaps the most widely used despite their being fraught with assumptions and potential pitfalls. Requirements for robust inferences of ancestral traits in general (i.e. those applicable to all types of characters) include accurate and robust phylogenetic hypotheses, complete species-level sampling and the appropriate choice of optimality criterion. Ecological characters, however, also require careful consideration of methods for accounting for intraspecific variability. Such methods include 'Presence Coding' and 'Polymorphism Coding' for discrete ecological characters, and 'Range Coding' and 'MaxMin Coding' for continuously variable characters. Ultimately, however, historical inferences such as these are, as with phylogenetic inference itself, associated with a degree of uncertainty. Statistically based uncertainty estimates are available within the context of model-based inference (e.g. maximum likelihood and Bayesian); however, these measures are only as reliable as the chosen model is appropriate. Although generally thought to preclude the possibility of measuring relative uncertainty or support for alternative possible reconstructions, certain useful non-statistical support measures (i.e. 'Sharkey support' and 'Parsimony support') are applicable to parsimony reconstructions.