A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa

Despite its large size (about 700 species), the australy-centred sedge tribe Schoeneae has received little explicit phylogenetic study, especially using molecular data. As a result, generic relationships are poorly understood, and even the monophyly of the tribe is open to question. In this study, plastid DNA sequences (rbcL, trnL-trnF, and rps16) drawn from a broad array of Schoeneae are analysed using Bayesian and parsimony-based approaches to infer a framework phylogeny for the tribe. Both analytical methods broadly support the monophyly of Schoeneae, Bayesian methods doing so with good support. Within the schoenoid clade, there is strong support for a series of monophyletic generic groupings whose interrelationships are unclear. These lineages form a large polytomy at the base of Schoeneae that may be indicative of past radiation, probably following the fragmentation of Gondwana. Most of these lineages contain both African and non-African members, suggesting a history of intercontinental dispersal. The results of this study clearly identify the relationships of the African-endemic schoenoid genera and demonstrate that the African-Australasian genus Tetraria, like Costularia, is polyphyletic. This pattern is morphologically consistent and suggests that these genera require realignment.     

Two new leafless species of Ficinia (Cypereae,Cyperaceae) from the Greater Cape Floristic Region of South Africa

Two new species of Ficinia (Cypereae, Cyperaceae) are described from South Africa. Ficinia has its centre of diversity in the Greater Cape Floristic Region (GCFR), with c. 90% of the species growing in the Fynbos biome. Recent collections from the arid edge of the Fynbos biome and in the Succulent Karoo biome have revealed two species new to science. Both are perennial plants that lack leaf blades and have sticky leaf sheaths.     

Two new species of Asteraceae (tribe Anthemideae,subtribe Pentziinae) from the Cape Floristic Region of South Africa

Two new species of Asteraceae (tribe Anthemideae, subtribe Pentziinae) from the Cape Floristic Region of South Africa are described. Marasmodes schlechteri Magee & J.C.Manning, a local endemic from the lowlands between Piketberg and the Olifants River Mountains, is distinguished by its spreading leaves with axillary fascicles and relatively large, solitary capitula with obconical involucre borne on very short lateral shoots. Pentzia trifida Schltr. ex. Magee & J.C.Manning is a well-collected limestone fynbos endemic that is readily distinguished by the regularly trifid leaves, broadly cyathiform involucres with lanceolate to oblanceolate bracts, and the well developed pappus extending the entire length of the relatively short corolla tube.     

Identifying spatial components of ecological and evolutionary processes for regional conservation planning in the Cape Floristic Region, South Africa

Abstract. Conservation seeks ultimately to protect and maintain biodiversity indefinitely. Most biodiversity features targeted in past conservation planning have been largely aspects of ecological and biogeographical pattern rather than process. However, the persistence of biodiversity can only be ensured through consideration of the ecological and evolutionary processes that underpin biodiversity, as well as its present spatial pattern. This paper identifies spatial surrogates of ecological and evolutionary processes for regional conservation planning in one of the world's biodiversity hotspots, the Cape Floristic Region. We identified six types of spatial components (namely edaphic interfaces, upland–lowland interfaces, sand movement corridors, riverine corridors, upland–lowland gradients and macroclimatic gradients) as surrogates for key processes such as ecological and geographical diversification, and species migration. Spatial components were identified in a GIS using published data and expert knowledge. Options for achieving targets for process components have been seriously compromised by habitat transformation. Between 30 and 75% of the original extent of the spatial components currently remain functional. Options for achieving upland–lowland and macroclimatic gradients are very limited in the lowlands where most of the habitat has been transformed by agriculture. We recommend that future studies place their research on ecological and evolutionary processes in a spatially explicit framework. Areas maintaining adaptive diversification (e.g. environmental gradients, ecotones) or containing historically isolated populations should be identified and protected. The spatial dimensions of eco-logical processes such as drought and fire refugia also need to be determined and such insights incorporated in conservation planning. Finally, connectivity within these areas should be ensured to maintain species migration and gene flow.     

Potential impact of viticulture expansion on habitat types in the Cape Floristic Region, South Africa

The wine industry in the Western Cape, South Africa has expanded over the past decade, particularly since the lifting of trade sanctions in 1992. Wine grapes are cultivated on fertile soils upon which threatened biodiversity habitat units of the Cape Floristic Region occur naturally. There is a concern as to whether further expansion of the wine industry, which would benefit the economy through increased foreign exchange, would encroach on the little remaining vegetation in vineyard-producing areas. Predictive land use modeling using logistic regression techniques was applied to determine suitable areas for vineyard cultivation according to climatic, topographic, and soil/geology variables. Of the most threatened habitats, 14849 hectares are particularly suitable for vineyards. Breede fynbos/renosterveld mosaic was the habitat most likely to be converted, and was considered 89.3% irreplaceable to current conservation goals. Also vulnerable are Ashton inland renosterveld and Boland coast renosterveld, the latter being 100% irreplaceable. Although the high rate in vine replanting suggests that the need for untransformed land will not be great immediately, an economic analysis showed that protection of these areas against future ploughing will be vital if targets of adequately representing each habitat in the Cape Floristic Region are to be met. Land use change modeling, especially if done in a spatially explicit and integrated manner with expert input, was shown to be an important technique for the extrapolation of historical patterns to understand the forces that shape landscapes, allowing for the assessment of management alternatives, and testing our understanding of key processes in land use changes that effect conservation planning.     

Climate change drives speciation in the southern rock agama (Agama atra) in the Cape Floristic Region, South Africa

Aim Vicariance has played a major role in the evolution of the southern rock agama, Agama atra (Reptilia: Agamidae), and it is hypothesized that habitat shifts will affect small‐scale patterns of gene flow. The Cape Floristic Region (CFR) is known for high levels of diversity and endemism; thus we set out to investigate whether genetic structuring of CFR populations of A. atra corresponds to regional environmental shifts. Location Cape Fold Mountains and the Cape Floristic Region of South Africa. Methods The phylogeographical structure of 116 individuals of A. atra was determined by making use of 988 characters derived from two mitochondrial DNA fragments (control region and the NADH dehydrogenase subunit 2 coding region, ND2). Most animals originated from the CFR, but to gain a better understanding of the processes and patterns of dispersal within the species, 17 additional specimens from outside the CFR were also included and analysed in a phylogenetic context. Results Parsimony and Bayesian analyses revealed four distinct CFR clades (Cape clades) associated with geography. Phylogenetic analyses suggest that populations of A. atra in the CFR region are not entirely isolated from other populations, because some individuals from outside the CFR were nested within the four main Cape clades. The combined mitochondrial DNA data set revealed 59 distinct haplotypes in the CFR. Analysis of molecular variance (amova ) confirmed the high degree of genetic structure among the Cape clades, with more than 75% of the genetic variation found among the geographical areas. A spatial amova suggested that a ‘central clade’ originally defined as one of the four Cape clades may contain several additional populations. The main cladogenesis of A. atra within the CFR is estimated to have taken place c. 0.64–2.36 Ma. Main conclusions Agama atra shows at least four distinct genetic provinces within the CFR region, which highlights the conservation importance of this biologically diverse area. The dates of separation among the clades coincide well with the documented Pleistocene climate fluctuations, which might have contributed towards the isolation among lineages; the congruent genetic structure of A. atra with other CFR taxa further supports vicariance as a main isolating factor.     

Analysis of active rotenone concentration during treatment of the Rondegat River,Cape Floristic Region,South Africa

Most endemic freshwater fish species of the Cape Floristic Region are listed as threatened, due mainly to the impacts of invasive alien fish species. The piscicide rotenone has been identified as a potential tool to aid the conservation of indigenous species through the removal of invasive fish. Rotenone was used in the Rondegat River, Cederberg, where smallmouth bass Micropterus dolomieu had extirpated the indigenous fish. An initial rotenone treatment in March 2012 was followed by another in March 2013. Due to concerns following the first treatment about possible build-up of rotenone between treatment stations, the second treatment included monitoring of rotenone concentrations during the treatment. Measured concentrations were consistently below the selected treatment concentration of 37.5 µg l^?1 and dropped to below the tested effective piscicidal concentration of 12.5 µg l^?1 at some sampling points. There was no build-up of rotenone within the treatment zones, but rotenone took longer than expected to clear out of the treatment area. The rotenone was effectively neutralised when the neutralisation station was operational, but was still detectable after neutralisation was terminated.     

Athanasia argentea and A. gyrosa (Asteraceae), two new species from the Cape Floristic Region of South Africa

Two new species of Athanasia (Asteraceae) from the Swartruggens Mountains in the Cape Floristic Region (CFR) of South Africa are described. Athanasia argentea is distinguished by the closely imbricate leaf arrangement, the canescent, curved to geniculate leaves and solitary capitula; and Athanasia gyrosa, by the closely imbricate, spiral leaf arrangement, capitula not apically constricted, and relatively large cypselas with ribs extending into apical horns.     

A pragmatic approach to estimating the distributions and spatial requirements of the medium- to large-sized mammals in the Cape Floristic Region, South Africa

Conservation planning in the Cape Floristic Region, a recognized world plant diversity hotspot, required systematic information on the estimated distributions and spatial requirements of the medium- to large-sized mammals within each of 102 Broad Habitat Units delineated according to key biophysical parameters. As a consequence of a general lack of data, we derived a pragmatic approach for obtaining estimates of these two parameters. Distribution estimates were based on a combination of a literature survey (with emphasis on early texts) and the ecological requirements of the species. Spatial requirement estimates were derived from a simple spreadsheet model that is based on forage availability estimates and the metabolic requirements of the mammals in question. Our analysis incorporated adaptations of the agriculture-based Large Stock Unit or Animal Unit approach. The predictions of the model were tested by comparing them with actual density data. The outcomes provided realistic estimates of the two parameters. However, they should be considered as testable hypotheses and the concept of adaptive management — or management by hypothesis — must apply. Examples of the outcomes are provided in the form of maps and tables.     

Disa albomagentea (Orchidaceae), a new species from the Hottentots Holland Mountains in the Cape Floristic Region, South Africa

A new orchid, Disa albomagentea, is described from the Hottentots Holland Mountains in the Western Cape Province of South Africa. It is an obligately fire-dependent species closely related to Disa obtusa (sect. Disella), from which it can be easily distinguished by the larger flowers, i.e. galea 7-9 mm long versus 4-7 mm long, which are patent and bicoloured, i.e. magenta, white and not spotted versus purple brown, white to cream to greenish, and variously purple spotted. It appears to be endemic to seeps and marshes on the high peaks.     

Molecular and morphological evidence for a new species from South Africa: Carex rainbowii (Cyperaceae)

Carex rainbowii (Cariceae, Cyperaceae), a new species from the Drakensberg mountains (KwaZulu-Natal province), is described and illustrated. It was found in the shady understory of the Afromontane forest in the Cathedral Peak area. An additional, nearby population was also identified based on previously collected herbarium material. Morphological and molecular (cpDNA 5′trnK intron and nrDNA ITS and ETS sequences) data were used to evaluate the taxonomic status of these populations and shed light on their systematic placement. Our data strongly support their taxonomic identity and inclusion in Carex sect. Sylvaticae. The new species can be readily distinguished from other related taxa mainly by the frequently androgynecandrous terminal spike, dense female spikes, hyaline glumes, as well as by some quantitative features. This finding implies a considerable biogeographic disjunction from the mainly Eurasian-North African range of the remaining species of sect. Sylvaticae, a pattern also found in the related sections Ceratocystis, Rhynchocystis and Spirostachyae. Comments are provided on previous misidentifications of C. rainbowii as the closely related Carex sylvatica. Data pertinent to the conservation status of the species are provided.     

Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences

Within the tribe Schoeneae (Cyperaceae), the relationships between Carpha and its relatives have not been certain, and the limits and definition of Carpha have been controversial. Further, the relationships of species within Carpha have been unclear. In this study, cladistic analyses based on chloroplast trnL intron and trnL-trnF intergenic spacer sequence data were undertaken to estimate phylogenetic relationships in and around Carpha. This study found that Trianoptiles is sister to Carpha; Ptilothrix is sister to Cyathochaeta rather than to Carpha as suggested by some former authors; and Gymnoschoenus is distant from Carpha and its close relatives. The merging of Schoenoides back into Oreobolus is supported. The findings also revealed the non-monophyletic status of Costularia and of Schoenus, and indicated the phylogenetic relationships of species within Carpha.     

Later Stone Age human hair from Vaalkrans Shelter,Cape Floristic Region of South Africa,reveals genetic affinity to Khoe groups

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter–gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry “Coloured” groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.     

Insect species richness tracking plant species richness in a diverse flora: gall-insects in the Cape Floristic Region, South Africa

The Cape Floristic Region (CFR) is one of the most plant-species-rich regions in the world. It is also a warm temperate region and hypothetically should have high gall-insect species richness, making it interesting to investigate the relationship between the insects of the region and the rich flora. The relationship between gall-insect species richness (GSR) and plant richness was investigated for the Fynbos and for representatives of vegetation of the whole CFR. Samples (of up to 600 plants per transect for Fynbos) of woody shrubs were investigated for the presence of galls. The species richness of these insects was quantified, as well as plant species richness for each transect. GSR for Fynbos was compared to global figures for GSR. Fynbos harboured significantly more gall-insect species than other CFR vegetation types. GSR was positively correlated with CFR plant richness. GSR also closely tracked plant richness in Fynbos. GSR was not significantly influenced by other variables (elevation and aspect), suggesting that plant richness per se was an important factor in generating GSR. Fynbos GSR is comparable to other sclerophyllous regions of high GSR globally, corroborating that this vegetation type is conducive to gall-insect diversification. There is likely to be a high percentage of gall-insect endemism in the Fynbos, as might be expected from the high host fidelity of this insect group. Received: 22 September 1997 / Accepted: 16 February 1998