Stable climate corridors promote gene flow in the Cape sand snake species complex (Psammophiidae)

Climate shifts during the Quaternary Period have driven changes in regional range dynamics for many species, influencing population structure of species and in some cases promoting speciation. Within southern Africa, the psammophine snakes Psammophis trinasalis and P. namibensis were historically considered subspecies of P. leightoni but were elevated to species rank based on ecological differences. Preliminary phylogenetic analyses suggested intraspecific, not interspecific genetic variation between these taxa, but this finding was based on very limited data and could not be confirmed. To assess the level of genetic differentiation within the P. leightoni species complex, we explored the evolutionary history of these snakes by combining phylogenetic analyses, species distribution modelling and an examination of morphology. We generated a comprehensive, multi-gene phylogeny for Psammophis that included wider geographic sampling of the three species in the complex. Using this phylogeny, Bayesian and distance-based species delimitation analyses showed intraspecific, not interspecific divergences between taxa in the complex, suggesting that they collectively represent a single taxon. Furthermore, non-metric multidimensional scaling analysis of scalation characters showed no differences between the species. Moreover, palaeo-modelling at three time periods since the last interglacial period suggest that there have been varying levels of connectivity between these taxa, which has likely facilitated gene flow between them. Given the evidence, we propose that the P. leightoni complex represents a single species and therefore formally synonymise the three species.     

Geographical affinities of the Cape flora, South Africa

Aim The flora characteristic of the Cape Floristic Region (CFR) is dominated by a relatively small number of clades that have been proposed as ‘Cape clades’. These clades have variously been suggested to have African or Austral affinities. Here we evaluate the support for these conflicting hypotheses. In addition, we test the hypothesis that these clades share a common time of differentiation from their geographical neighbours. Location The Cape Floristic Region, South Africa Methods We use both published and unpublished phylogenetic information to investigate the geographical sister areas of the Cape clades as well as the timing and the direction of biogeographical disjunctions. Results Almost half of the Cape clades for which unambiguous sister areas could be established show a trans‐Indian Ocean disjunction. The earliest trans‐Indian Ocean disjunction dates from 80 Ma. Other disjunctions date from various times in the Cenozoic, and we suggest that the process of recruiting lineages into the Cape flora might be ongoing. Relatively few Cape clades show a sister relationship with South America and tropical Africa, despite their relative geographical proximity. Numerous Cape clades contain species also found on tropical African mountains; in all cases tested, these species are shown to be embedded within the Cape clades. While many Cape clades show a relationship with the Eurasian temperate flora, this is complicated by their presence in tropical Africa. The single case study addressing this to date suggests that the Cape clade is nested within a European grade. Main conclusions Although many Cape clades show Austral rather than African relationships, there are numerous other patterns suggestive of a cosmopolitan flora. This spatial variation is echoed in the temporal data, from which, although there is wide variance around the dates of disjunctions, it is clear the Cape flora has been assembled over a long time period. There is no simple hypothesis that can account for the geographical sources of the currently distinctive Cape flora. The phylogenetic positions of Afromontane members of Cape clades suggest a history of dispersal from the CFR, rather than the reverse.     

Habitat heterogeneity drives the host‐diversity‐begets‐parasite‐diversity relationship: evidence from experimental and field studies

Despite a century of research into the factors that generate and maintain biodiversity, we know remarkably little about the drivers of parasite diversity. To identify the mechanisms governing parasite diversity, we combined surveys of 8100 amphibian hosts with an outdoor experiment that tested theory developed for free‐living species. Our analyses revealed that parasite diversity increased consistently with host diversity due to habitat (i.e. host) heterogeneity, with secondary contributions from parasite colonisation and host abundance. Results of the experiment, in which host diversity was manipulated while parasite colonisation and host abundance were fixed, further reinforced this conclusion. Finally, the coefficient of host diversity on parasite diversity increased with spatial grain, which was driven by differences in their species–area curves: while host richness quickly saturated, parasite richness continued to increase with neighbourhood size. These results offer mechanistic insights into drivers of parasite diversity and provide a hierarchical framework for multi‐scale disease research.     

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.     

Distribution patterns of the Diaptomidae (Calanoida: Copepoda) in southern Africa

All freshwater calanoids in southern Africa belong to the family Diaptomidae of which there are two subfamilies, the Paradiaptominae (Lovenula, Paradiaptomus and Metadiaptomus) and Diaptominae (Tropodiaptomus and Thermodiaptomus). The Paradiaptominae are endemic to Africa, while the Diaptominae have one endemic African genus Thermodiaptomus, and the other genus Tropodiaptomus, occurs in other parts of the world as well as Africa. Knowledge of distribution of the Diaptomidae has been hampered by incomplete taxonomic knowledge and lack of co-ordination of available information. Distribution patterns of 19 described species and 11 new species confirm that the majority of species have a limited distribution, and that the Paradiaptominae are arid-adapted and belong to temporary pool communities. Six species are endemic to coastal pans and vleis of the western and southern Cape Province. Only those species with a wider distribution have been recorded as colonising man-made lakes. The four Lovenula species are predators and often co-exist with a Metadiaptomus species as prey. Synapomorphies of widely separated species of the Paradiaptominae, provide interesting insights into how their evolution may have been governed by vicariance, dispersal and palaeoenvironments of the African continent.     

Experimental biogeography: the role of environmental gradients in high geographic diversity in Cape Proteaceae

One of the fundamental dimensions of biodiversity is the rate of species turnover across geographic distance. The Cape Floristic Region of South Africa has exceptionally high geographic species turnover, much of which is associated with groups of closely related species with mostly or completely non-overlapping distributions. A basic unresolved question about biodiversity in this global hotspot is the relative importance of ecological gradients in generating and maintaining high geographic turnover in the region. We used reciprocal transplant experiments to test the extent to which abiotic environmental factors may limit the distributions of a group of closely related species in the genus Protea (Proteaceae), and thus elevate species turnover in this diverse, iconic family. We tested whether these species have a “home site advantage” in demographic rates (germination, growth, mortality), and also parameterized stage-structured demographic models for the species. Two of the three native species were predicted to have a demographic advantage at their home sites. The models also predicted, however, that species could maintain positive population growth rates at sites beyond their current distribution limits. Thus the experiment suggests that abiotic limitation under current environmental conditions does not fully explain the observed distribution limits or resulting biogeographic pattern. One potentially important mechanism is dispersal limitation, which is consistent with estimates based on genetic data and mechanistic dispersal models, though other mechanisms including competition may also play a role. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies

Phylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations, are reviewed. Sampling of genes, genomes and species are considered. Although increased higher-level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.     

Using habitat models to map diversity: pan-African species richness of ticks (Acari: Ixodida)

Aims To show how logistic regression models for individual species can be used to produce improved estimates of species richness at a continental scale; to present these data for African ticks (Acari: Ixodida); and to address the question of whether there is a latitudinal gradient in tick species richness. Location Africa. Methods A database of 34,060 collection records for African ticks is used to produce a pan‐African map of known tick species richness at 0.25 × 0.25‐degree resolution. The likely distributions of seventy‐three species are then estimated from environmental factors using logistic regression, and localities where there is a suitably high probability of occurrence for a given species are added to the original data for that species. These augmented data are combined to produce a map of the predicted pan‐African distribution of tick species richness. The relationship of species richness to latitude is considered along a transect placed across some of the more extensively collected areas. Results Maps of known and predicted pan‐African tick species richness are presented, and deficiencies in the available data are highlighted. Correlations using both known and predicted estimates of tick species richness suggest that ticks follow similar species richness patterns to those described for African mammals and birds, with a latitudinal gradient and highest species richness in east equatorial Africa. Tick species ranges are log‐normally distributed. Main conclusions Carefully constructed probability surfaces offer a more powerful approach to mapping species ranges than simple presence‐absence maps. Such models are a useful extension to current biogeographical methods and have a wide range of potential applications in ecology, epidemiology and conservation. Tick species richness at a continental scale follows similar trends to those reported for mammals and birds.     

Waterbird assemblages and associated habitat characteristics of farm ponds in the Western Cape, South Africa

Natural freshwater wetlands are among the most threatened habitats on Earth. Effective wetland biodiversity conservation can not, however, be evaluated without fully understanding the roles of artificial waterbodies as refuges for water-dependent plants and animals. Waterbird assemblages were examined on 59 farm ponds in the Elgin and Caledon districts of the Western Cape, South Africa. This study examines the relationship between waterbird use and habitat characteristics of farm ponds. Patterns of temporal and spatial variation of waterbird species richness and abundance were quantified in relation to the habitat characteristics of each pond. Cluster analysis and multiple regression analyses identified surface area of the farm ponds as an important variable determining the presence and abundance of many waterbird species. Structural diversity in terms of vegetation in and around the ponds was especially important in determining their usage by waterbirds. These variables were evaluated in terms of creating a mosaic of habitat types (by varying vegetation structure and pond topography), which may be a useful way to enhance waterbird diversity at farm ponds. This study concludes that the high number of farm ponds in the transformed habitat matrix of the Western Cape plays an important role in conserving waterbirds.     

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.     

Isolation and high genetic diversity in dwarf mountain toads (Capensibufo) from South Africa

Traditional models of amphibian dispersal and gene flow point to low dispersal and high philopatry. In recent years, this traditional view has been challenged and it appears that no general model holds across taxa. Conservation of amphibians cannot be addressed on an over‐arching scale, but must come on a case‐by‐case basis, especially for range‐restricted species where information on gene flow and migration must be incorporated into conservation efforts. The only two members of the genus Capensibufo Grandison, 1980 (Anura: Bufonidae) are range restricted small bufonids, with distributions limited to montane areas in South Africa. Using a Bayesian analysis of two mitochondrial markers (16S and ND2), we examined the genetic patterns in Capensibufo rosei and Capensibufo tradouwi in order to understand both taxonomic and geographic boundaries. These species were not monophyletic, and demonstrate no clear taxonomic boundaries. Instead, the genus is extremely diverse genetically, with distinct lineages confined to isolated mountains that represent geographic boundaries. In addition, bioclimatic modelling using MAXENT and scenarios of climatic conditions at both the present and last glacial maximum suggest multiple bioclimatic and physical barriers to gene flow at present and in the past. We conclude that members of the genus have very low vagility, that current taxonomic boundaries are inadequate, and that strong geographic structuring has undoubtedly contributed to genetic diversity at the species level, rather than the population level. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 822–834.     

Leaf shape and size track habitat transitions across forest–grassland boundaries in the grass family (Poaceae)

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest‐associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest–grassland biome boundaries.     

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.     

Here be dragons: a phylogenetic and biogeographical study of the Smaug warreni species complex (Squamata: Cordylidae) in southern Africa

Taxonomy of the Smaug warreni species complex remains contentious despite known morphological differences and geographical separation of the various taxa. This study uses an 11‐gene dataset to recover phylogenetic relationships between the seven nominal members of the S. warreni complex. Eight well‐supported clades were returned, with S. warreni barbertonensis found to be paraphyletic. A time‐calibrated analysis of molecular data indicates that all eight clades in the S. warreni complex separated in the late Miocene, much earlier than the date suggested by the existing hypothesis of vicariance through the ingression of Kalahari sands. Ecological niche modelling indicates that although all clades are allopatric, a slight decrease in temperature could potentially render them sympatric, supporting an hypothesis of range expansion through climatic change. © 2014 The Linnean Society of London