Input data, analytical methods and biogeography of Elegia (Restionaceae)

Aim The aim of this paper is to determine the optimal methods for delimiting areas of endemism for Elegia L. (Restionaceae), an endemic genus of the Cape Floristic Region. We assess two methods of scoring the data (presence–absence in regular grids, or in irregular eco‐geographical regions) and three methods for locating biogeographical centres or areas of endemism, and evaluate one method for locating biotic elements. Location The Cape Floristic Region (CFR), South Africa. Methods The distribution of all 48 species of Elegia was mapped as presence–absence data on a quarter‐degree grid and on broad habitat units (eco‐geographical areas). Three methods to delimit areas of endemism were applied: parsimony analysis of endemism (PAE), phenetic cluster analysis, and NDM (‘end em ism’). In addition, we used presence–absence clustering (‘Prabclus’) to delimit biotic elements. The performances of these methods in elucidating the geographical patterns in Elegia were compared, for both types of input data, by evaluating their efficacy in maximizing the proportion of endemics and the number of areas of endemism. Results Eco‐geographical areas perform better than quarter‐degree grids. The eco‐geographical areas are potentially more likely to track the distribution of species. The phenetic approach performed best in terms of its ability to delimit areas of endemism in the study area. The species richness and the richness of range‐restricted species are each highest in the south‐western part of the CFR, decreasing to the north and east. The phytogeographical centres identified in the present study are the northern mountains, the southern mountains (inclusive of the Riviersonderend Mountains and the Cape Peninsula), the Langeberg range, the south coast, the Cape flats, and the west coast. Main conclusions This study demonstrates that (1) eco‐geographical areas should be preferred over a grid overlay in the study of biogeographical patterns, (2) phenetic clustering is the most suitable analytical method for finding areas of endemism, and (3) delimiting biotic elements does not contribute to an understanding of the biogeographical pattern in Elegia. The areas of endemism in Elegia are largely similar to those described in other studies, but there are many detailed differences.     

Stimulation of seed germination in South African species of Restionaceae by plant-derived smoke

The Restionaceae is one of the three major families defining fynbos, the characteristic vegetation type of the Cape Floristic Region. Periodic fires with a frequency of 5 to 40 years are a natural phenomenon in fynbos vegetation. Fire-stimulated seed germination has been reported for a variety of fynbos species, and species in the Asteraceae, Ericaceae, Proteaceae and Restionaceae have shown a germination response to smoke and/or aqueous smoke extracts. In the present study seed of 32 species was screened to obtain an indication of how important the smoke cue is for germination in the South African Restionaceae. The results of the present study represents the first occasion that comparative germination data for South African species in this family have ever been obtained. Twenty-five of the 32 species tested showed a statistically significant improvement in germination following smoke treatment. Untreated seeds of 18 of the species responding, showed a high degree of dormancy with only 0.1% to 2.0% germination. These results suggest that under natural conditions smoke from fynbos fires may provide an important cue for triggering seed germination in this family. The degree of improvement in germination following smoke treatment ranged from 147% in the case of Restio festuciformis to 25300% in the case of Rhodocoma capensis. It is suggested that the 16 species which showed a 1000% or more increase in germination following smoke treatment form a group in which smoke is likely to be the major cue for germination. In those species in which there is a lesser response, smoke may be one of a number of germination cues which include heat, and possibly alternating high and low incubation temperatures. The four species that did not germinate were all myrmecochorus, nut-fruited species. More information is needed concerning the fire survival strategy of South African Restionaceae species and many more will have to be investigated in the nursery and in the field, before the full pattern of response within the family and its significance can be elucidated.     

Contrasting patterns of radiation in African and Australian Restionaceae

The floras of the Mediterranean-climate areas of southern Africa and southwestern Australia are remarkably species rich. Because the two areas are at similar latitudes and in similar positions on their respective continents, they have probably had similar Cenozoic climatic histories. Here we test the prediction that the evolution of the species richness in the two areas followed a similar temporal progression by comparing the rates of lineage accumulation for African and Australian Restionaceae. Restionaceae (Poales) are typical and often dominant elements in the fynbos vegetation of the Cape Floristic Region of southern Africa and the kwongan vegetation of the Southwestern Floristic Province of Western Australia. The phylogeny of the family was estimated from combined datasets for rbcL and trnL-F sequences and a large morphological dataset; these datasets are largely congruent. The monophyly of Restionaceae is supported and a basal division into an African clade (approximately 350 species) and an Australian clade (146 species) corroborated. There is also support for a futher subdivision of these two large sister-clades, but the terminal resolution within the African clade is very weak. Fossil pollen records provided a minimum age of the common ancestor of Australian and African Restionaceae as 64-71 million years ago, and this date was used to calibrate a molecular clock. A molecular clock was rejected by a likelihood ratio test; therefore, rate changes between the lineages were smoothed using nonparametric rate smoothing. The rate-corrected ages were used to construct a plot of lineages through time. During the Palaeogene the Australian lineage diversity increased consistent with the predictions of the constant birthrate model, while the African lineage diversity showed a dramatic increase in diversification rate in the Miocene. Incomplete sampling obscures the patterns in the Neogene, but extending the trends to the modern extant diversity suggests that this acceleration in the speciation rate continued in the African clade, whereas the Australian clade retained a constant diversification rate. The substantial morphological and anatomical similarity between the African and Australian Restionaceae appear to preclude morphological innovations as possible explanations for the intercontinental differences. Most likely these differences are due to the greater geographical extent and ecological variation in temperate Australia than temperate Africa, which might have provided refugia for basal Restionaceae lineages, whereas the more mountainous terrain of southern Africa might have provided the selective regimes for a more rapid, recent speciation.     

Insect diversity in Cape fynbos and neighbouring South African vegetation

Aim  It has often been suggested that South Africa's Cape fynbos shrublands, although extremely rich in plant species, are poor in insects, thus representing a notable exception from the broad plant–insect diversity relationship. The aims of this study were to compare the diversity patterns of plant-inhabiting insects in fynbos and the vegetation of three neighbouring biomes (grassland, subtropical thicket, and Nama-karoo), and to test for a general relationship between plant diversity and insect diversity across these biomes.
Location  South-western to south-eastern South Africa.
Methods  We conducted seasonal plant surveys and sweep insect sampling in 10 × 10 m plots in the Baviaanskloof Conservation Area (Eastern Cape), where all four biomes occur. We also conducted once-only collections in the core area of each biome.
Results  Fynbos plots had insect diversity values similar to those of grassland and subtropical thicket (a dense, evergreen and spinescent shrubland with a high abundance of succulents and climbers), and significantly higher than Nama-karoo (an open, semiarid shrubland). A remarkably strong positive relationship was found between plant and insect species richness.
Main conclusions  Previous generalizations were based on a few insect groups (e.g. butterflies, under-represented in fynbos), but ignored published results on other groups (e.g. galling insects, which are in fact over-represented in this vegetation). We show that, overall, insect diversity in fynbos is comparable to that of neighbouring biomes. Fynbos vegetation does not represent a significant exception from the broad positive relationship between plant diversity and insect diversity.     

Phylogeny and evolution of the South African genus Metalasia (Asteraceae–Gnaphalieae) inferred from molecular and morphological data

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the ‘Metalasia clade’. A species‐level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA‐trnH, trnL‐trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well‐supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M. densa which appears to be an intricate species complex. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 173–198.     

Genomics of the divergence continuum in an African plant biodiversity hotspot,I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species‐rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species‐rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non‐neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.     

Othonna cerarioides (Asteraceae: Othonnineae), a new species from Namaqualand,South Africa

Othonna cerarioides Magoswana and J.C. Manning is described as a new species from Namaqualand, Northern Cape Province of South Africa. It is an erect shrub with rod-like stems and branches, bearing numerous spur-shoots with obovate-oblanceolate leaves clustered at the tips, and up to nine disciform capitula per spur-shoot. Othonna cerarioides is anomalous in the genus in that the style of some of the disc florets is bifid. Othonna is diagnosed within subtribe Othonnineae by female-sterile disc florets with simple (or very rarely minutely bifid) styles. The disc florets in the closely related genus Hertia are bisexual with well branched styles.     

Water availability,fundamental niches and realized niches: A case study from the Cape flora

The ability of plants to survive drought or waterlogging constitutes an important niche parameter, which might be particularly significant in explaining species coexistence in the species‐rich and seasonally dry Cape Floristic Region of South Africa. However, the degree of physiological adaptation and specialization to these eco‐hydrological parameters (the fundamental niche) cannot be readily inferred from correlative studies based on species distributions and spatial variation in environmental parameters (the realized niche). We used an ex situ greenhouse experiment to compare the fundamental hydrological niches (different mean annual precipitation, rainfall seasonality and soil drainage) of six eco‐hydrologically divergent African Restionaceae species. Juvenile plants were subjected to six different watering treatments, ranging from no watering to waterlogging, to determine drought and waterlogging susceptibility and optimal growth conditions. We used the rate of biomass accumulation and survival rate as response measures. We found that species from dry and mesic (but well‐drained) habitats had optimal or near‐optimal growth at benign conditions (under which most restio species grow well). All species performed worse when droughted and died when not watered. Species from dry habitats tended to perform better (assessed in growth) than species from wet habitats under droughting. Species from wet habitats performed best when waterlogged, whereas species from dry habitats performed very poorly when waterlogged – thus showing that realized and fundamental niches covaried at the wet end of the hydrological gradient. We conclude that eco‐hydrological parameters are part of the fundamental niche, and fundamental and realized species niches are approximately correlated along them. The distribution of wet habitat species appears not to reflect their drought tolerance, suggesting that it may not be predicted by bioclimatic variables, but rather by soil drainage characteristics.     

Bryobartramia schelpei T.A.Hedderson,a new species to accommodate the South African populations of the genus

Abstract

South African populations of Bryobartramia have been treated as B. novae-valesiae, a species otherwise restricted to Australia. However, material from the two regions differs in a number of traits, and the African populations are here described as a new species, B. schelpei. The Cape species differs most obviously from B. novae-valesiae in the markedly prorate-papillose, narrow, thick-walled cells of the calyptra. Nested analysis of variance reveals further morphometric differences, including the relatively narrower, more cylindrical, calyptra with a longer rostrum, and the smaller leaf cells and spores. Bryobartramia schelpii is known only from arid portions of the winter rainfall region in the Northern and Western Cape Provinces of South Africa.     

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     

Frequent and parallel habitat transitions as driver of unbounded radiations in the Cape flora

The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species‐level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter‐wet climate, or a recent density‐dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora.     

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.     

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.     

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.     

Floral Ontogenetic Evidence in Support of the Willdenowia Clade of South African Restionaceae

Willdenowia clade of Restionaceae was studied to understand patterns of reduction of floral elements and sample evidence for discussing the relationships of the group. All species studied are characterized by a concordant reductive trend involving the retardation/reduction of the perianth, the loss of the anterior carpel and the displacement of the remaining carpels, linked with a strongly compressed spikelet. Different modes of carpel reduction, such as a progressive or immediate loss, or fusion of two neighboring carpels, are presented and discussed. The most parsimonious event of gynoecium evolution for the Willdenowia clade is either the sterilization of two carpels in an originally trimerous gynoecium, followed by the loss of the anterior carpel, or the sudden loss of the anterior carpel, preceeding the sterilization of one lateral carpel. The concordant development of the taxa of the Willdenowia clade supports a one-time loss of a carpel and the homogeneity of the clade. Received 12 March 2001/ Accepted in revised form 29 May 2001     

Patterns of geophyte diversity and storage organ size in the winter-rainfall region of southern Africa

The winter‐rainfall region of southern Africa, covered largely by the fynbos and succulent karoo biomes, harbours the world's greatest concentration of geophyte species. Species diversity is greatest in the south‐west, where more than 500 species co‐occur in one quarter‐degree square; in the south‐east the values are generally around 100, and in the arid north‐west, always less than 50 (more often less than 10). In at least three species‐rich genera (Moraea, Eriospermum and Oxalis), the size of storage organs (bulbs, corms, tubers) varies inversely, with the largest average values occurring in the species‐poorer areas — both in the north‐western, and in the south‐eastern parts of the region. This negative correlation between average storage organ size and species diversity is, however, only observed at relatively large spatial scales, which suggests that there is no direct relationship between storage organ size and species diversity. More likely, both these measures are driven by winter rainfall amount and reliability, both of which peak in the south‐western Cape. We suggest that reliable winter rainfall makes large storage organs unnecessary and depresses extinction rates, thus leading to the accumulation of species.     

Correlates of hyperdiversity in southern African ice plants (Aizoaceae)

The exceptionally high plant diversity of the Greater Cape Floristic Region (GCFR) comprises a combination of ancient lineages and young radiations. A previous phylogenetic study of Aizoaceae subfamily Ruschioideae dated the radiation of this clade of > 1500 species in the GCFR to 3.8–8.7 Mya, establishing it as a flagship example of a diversification event triggered by the onset of a summer‐arid climate in the region. However, a more recent analysis found an older age for the Ruschioideae lineage (17 Mya), suggesting that the group may in fact have originated much before the aridification of the region 10–15 Mya. Here, we reassess the tempo of radiation of ice plants by using the most complete generic‐level phylogenetic tree for Aizoaceae to date, a revised calibration age and a new dating method. Our estimates of the age of the clade are even younger than initially thought (stem age 1.13–6.49 Mya), supporting the hypothesis that the radiation post‐dates the establishment of an arid environment in the GCFR and firmly placing the radiation among the fastest in angiosperms (diversification rate of 4.4 species per million years). We also statistically examine environmental and morphological correlates of richness in ice plants and find that diversity is strongly linked with precipitation, temperature, topographic complexity and the evolution of highly succulent leaves and wide‐band tracheids. © 2013 The Authors. Botanical Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 110–129.