Development and characterization of microsatellite loci for the tropical tree pathogen Botryosphaeria rhodina

Nineteen simple sequence repeat (SSR) markers were developed for the pathogen and blue stain fungus Botryosphaeria rhodina. Eight pairs were found to be polymorphic among isolates collected from Pinus spp., whereas a further five pairs were polymorphic when isolates from Pinus spp. were compared with those from Eucalyptus spp. Nine isolates of B. rhodina collected from pines and eucalypts in South Africa, Mexico and Indonesia were used to demonstrate the range of the markers. Testing the markers yielded preliminary evidence that relationships among isolates are more closely linked to host than to geographical origin.     

Is there genetic connectivity among the critically endangered White‐winged Flufftail (Sarothrura ayresi) populations from South Africa and Ethiopia?

The White‐winged Flufftail (Sarothrura ayresi) is known to occur in the highland marshes of Ethiopia, as well as almost 4000 km in South Africa. The White‐winged Flufftail is listed globally as Critically Endangered. In South Africa the population is estimated to be <50 birds. These birds are severely threatened by habitat destruction. Thus far, no genetic studies have been conducted on S. ayresi to confirm genetic connectivity between the South African and Ethiopian populations. In this study, analysis of mitochondrial and nuclear markers was conducted for White‐winged Flufftail samples from South African and Ethiopian birds, as well as Red‐chested Flufftail (Sarothrura rufa) for species comparison. Analyses of the DNA regions identified three variations between the two populations, supporting the hypothesis that these two populations are not different species or subspecies but are rather one migrating population with different seasonal occupied ranges. However, these results do not exclude the possibility of additional breeding and nonbreeding sites. Low genetic diversity in the populations of White‐winged Flufftails was observed, which needs to be further elucidated with fast evolving co‐dominant markers such as microsatellites, as this low diversity may ultimately contribute to the extinction of the species.     

A phylogeographic investigation of the kelp genus Laminaria (Laminariales,Phaeophyceae), with emphasis on the South Atlantic Ocean

The genus Laminaria has a wide distribution range compared with other kelp genera because it is found in both the North and the South Atlantic, on both sides of the North Pacific, as well as in the Mediterranean. Hypotheses behind this biogeographical pattern have been discussed by several authors but have not yet been fully evaluated with time‐calibrated phylogenies. Based on the analysis of four molecular markers (ITS2, rbcL, atp8 and trnWI), our goal was to reassess the Laminaria species diversity in South Africa, assess its relationship with the other species distributed in the South Atlantic and reconstruct the historical biogeography of the genus. Our results confirm the occurrence of a single species, L. pallida, in southern Africa, and its sister relationship with the North Atlantic L. ochroleuca. Both species belonged to a clade containing the other South Atlantic species: L. abyssalis from Brazil, and the Mediterranean L. rodriguezii. Our time‐calibrated phylogenies suggest that Laminaria originated in the northern Pacific around 25 mya, followed by at least two migration events through the Bering Strait after its opening (~5.32 mya). Today, the first is represented by L. solidungula in the Arctic, while the second gave rise to the rest of the Atlantic species. The colonization of the North Atlantic was followed by a gradual colonization southward along the west coast of Europe, into the Mediterranean (~2.07 mya) and two recent, but disconnected, migrations (~1.34 and 0.87 mya) across the equator, giving rise to L. abyssalis in Brazil and L. pallida in southern Africa, respectively.     

Pre-release evaluation of Heikertingerella sp. as a potential biocontrol agent for Tecoma stans in South Africa

Native to Central America, Tecoma stans (L.) Juss ex Kunth var. stans (Bignoniaceae) is a small tree that is invasive in South Africa and neighbouring countries. The plant was targeted for biological control in South Africa in 2003, with two insect agents released and established so far. The root-feeding flea beetle, Heikertingerella sp. (Coleoptera: Galerucinae: Alticini), was imported from Mexico as an additional biocontrol agent and its biology and host specificity was assessed under quarantine conditions. The beetle displayed a generation time (i.e. from adult to adult) of 49 to 67 days, ensuring four annual generations under laboratory conditions. The beetle's larval and adult stages inflicted high levels of damage on the root system and the leaves of T. stans, respectively. No-choice tests with 40 test-plant species revealed adult feeding on only two non-target species, Tecoma × alata and T. capensis (Thunb.) Spach, with feeding four times higher on T. stans. Larvae developed to adulthood on T. stans only. Multi-choice tests involving the three Tecoma species confirmed these trends, demonstrating that Heikertingerella sp. is host specific. Since T. × alata is a hybrid of T. stans with invasive tendencies, any unlikely attacks by Heikertingerella sp. would be inconsequential in South Africa. The native T. capensis, which suffered little leaf damage and produced no F1 adults, is also at minimal risk of attack. We conclude that Heikertingerella sp. is a suitable biocontrol agent for T. stans and that permission for its release in South Africa be sought.     

<Emphasis Type="Italic">Athyrium crassicaule</Emphasis> (<Emphasis Type="Italic">Woodsiaceae</Emphasis>), a new fern species from the Drakensberg,southern Africa

Summary  A new Athyrium species, A. crassicaule J. P. Roux (Woodsiaceae), is described from the Drakensberg in Lesotho and South Africa. A key to the Athyrium species in Lesotho, South Africa and Swaziland is provided.     

Biology,host range and varietal preference of the leaf-feeding geometrid, <Emphasis Type="Italic">Leptostales ignifera</Emphasis>, a potential biocontrol agent for <Emphasis Type="Italic">Lantana camara</Emphasis> in South Africa,under laboratory conditions

Lantana camara L. (Verbenaceae) is a weed of major importance in South Africa. It invades indigenous forests and veld, valuable commercial and agricultural forests, plantations and orchards, as well as river-catchment areas. Several natural enemies, including insect and pathogen species, have been released in South Africa, some of which established successfully. These do not exert sufficient control and additional natural enemies are required. Leptostales ignifera Warren (Lepidoptera: Geometridae), one of several new species being investigated as potential biocontrol agents, was collected in the subtropical parts of Florida, USA and Mexico. Host specificity trials indicated L. camara to be the preferred host plant of this quick-developing, voracious leaf-feeder, with some of the African indigenous Lippia species qualifying as very marginal hosts. The possible preference that L. ignifera might have for different South African naturalized L. camara varieties was studied during quarantine laboratory preference trials. Variety 029WP was the most suitable host for L. ignifera, although the other four tested varieties were able to support viable populations of the insect. Not taking other abiotic and biotic factors such as climate and predation into consideration, once released, L. ignifera should be able to establish on all five of the tested varieties in the field and contribute to the biological control of the complex of L. camara as a whole. Based on the above studies, permission has been granted for the release of L. ignifera in South Africa.     

Variation in host plant has no effect on the performance and fitness‐related traits of the specialist herbivore Pareuchaetes insulata

The effect of host plant dissimilarity on insect preference and performance was tested using two morphological forms of Chromolaena odorata (L.) King & Robinson (Asteraceae) (one from Florida, USA, another from South Africa), and a specialist herbivore, Pareuchaetes insulata (Walker) (Lepidoptera: Erebidae: Arctiinae) from Florida, USA, that was introduced as a biological control agent in South Africa. Although this insect did establish at one site, of some 21 sites at which over 800 000 individuals were released, its population level in the field has remained low after an initial outbreak in 2006. To explain the poor performance of P. insulata, we hypothesised that P. insulata larvae prefer Floridian C. odorata to the southern African C. odorata, which is morphologically and probably genetically distinct, and that larvae reared on Floridian C. odorata should have higher fitness and performance. We tested this by comparing insect performance metrics on each of the two plant forms in laboratory experiments. Apart from pupal mass, which was significantly greater on southern African C. odorata, P. insulata performance metrics were similar on both plant forms; there were no significant differences in total leaf area consumed, egg and larval development, immature survival rates, feeding index, host suitability index, growth index, and fecundity between the Floridian and southern African C. odorata plants. In sum, we could not demonstrate that differences in plant forms in C. odorata are responsible for the poor performance of P. insulata in South Africa.     

Genomewide gene‐associated microsatellite markers for the model invasive ascidian,Ciona intestinalis species complex

The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene‐associated microsatellite markers for C. intestinalis spA (=C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24–48), and Cape Town, South Africa (N = 24–33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from 2 to 11, 0 to 0.833 and 0.021 to 0.818, and from 2 to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross‐species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genomewide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genomewide resource for ecological and evolutionary studies using C. intestinalis as a model.     

Recent emergence and worldwide spread of the red tomato spider mite, <Emphasis Type="Italic">Tetranychus evansi</Emphasis>: genetic variation and multiple cryptic invasions

Plant biosecurity is increasingly challenged by emerging crop pests. The spider mite Tetranychus evansi has recently emerged as a new threat to solanaceous crops in Africa and the Mediterranean basin, with invasions characterized by a high reproductive output and an ability to withstand a wide range of temperatures. Mitochondrial (868 bp of COI) and nuclear (1,137 bp of ITS) loci were analyzed in T. evansi samples spanning the current geographical distribution to study the earliest stages of the invasive process. The two sets of markers separate the samples into two main clades that are only present together in South America and Southern Europe. The highest COI diversity was found in South America, consistent with the hypothesis of a South American origin of T. evansi. Among the invaded areas, the Mediterranean region displayed a high level of genetic diversity similar to that present in South America, that is likely the result of multiple colonization events. The invasions of Africa and Asia by T. evansi are characterized by a low genetic variation associated with distinct introductions. Genetic data demonstrate two different patterns of invasions: (1) populations in the Mediterranean basin that are a result of multiple cryptic introductions and (2) emerging invasions of Africa and Asia, each likely the result of propagules from one or limited sources. The recent invasions of T. evansi illustrate not only the importance of human activities in the spread of agricultural pests, but also the limits of international quarantine procedures, particularly for cryptic invasions.     

The rust mycobiota of southern Africa: Species richness, composition, and affinities

The rust mycobiota (Uredinales, Basidiomycota) of southern Africa (Botswana, Namibia, and South Africa) is analysed with regard to species richness, generic composition, and similarities to the rust mycobiotas of the remaining African continent and other regions of the world. Southern Africa is home to about 546 rust species: ca 522 species have been reported from South Africa, 73 from Namibia, and less than ten from Botswana. Thirty-two species were considered to be exotics. Two hundred and twenty-five of the species are restricted to southern Africa, suggesting an endemism rate of ca 44 %. At present, the rust fungus:host ratio is 1:38.5, which is much lower than expected from other regions of the world. This low ratio may partly be due to under-exploration of the area, but the results presented here indicate that a natural paucity of rust fungi on certain, especially species-rich plant taxa centred in southern Africa and possibly environmental factors are more important reasons. The predominant genera are Puccinia and Uromyces accounting for ca 59 % of the rust species. The genera Hemileia, Phakopsora and especially Ravenelia, centred in tropical regions, are well represented and sum up to 8 % of the species. Members of Melampsoraceae and Phragmidiaceae, common in temperate regions of the Northern Hemisphere, are scarce. Most of the other 28 recorded teleomorph genera are only represented by three or less species. In an African context, most species are shared with central and east Africa (almost 16 %). Only a few species are disjunct between southern and West Africa or Madagascar. Ca 10 % of the species are shared only with other parts of the paleotropics, especially the Indian subcontinent. Disjunctions of native species with the New World, Australia/New Zealand, or Europe are rare.     

Genetic diversity and maternal origin of Northeast African and South American donkey populations

To investigate the mtDNA variation and origin of maternal lineages in South American donkeys and to reassess the domestication of donkeys in northeast Africa, we analyzed sequences (489 bp of the D‐loop) from 323 domestic donkeys sampled from Peru, Brazil, Ethiopia and Egypt. Altogether, the 323 sequences displayed 53 different haplotypes (45 in Ethiopia, 14 in Egypt, eight in Peru and six in Brazil). Among the four populations, Egyptian donkeys possessed the highest haplotype diversity (0.910 ± 0.032), followed by Brazilian donkeys (0.879 ± 0.060). The Clade I haplotypes dominated in Peruvian donkeys (65%), whereas Clade II haplotypes dominated in Brazilian donkeys (67%). Estimates of F_ST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (F_ST = 0.4066), which could be explained by the complex introduction history of South American donkeys. Phylogeographic analysis indicates that northeast Africa could be the most probable domestication center for Clade I donkeys. Analysis of molecular variance confirmed a weak genetic structure in domestic donkey populations among four continents (Europe, Asia, Africa and South America).     

Smoke and heat: influence on seedling emergence from the germinable soil seed bank of mesic grassland in South Africa

We examined if germination and seedling emergence of species from the soil seed bank of mesic grassland in South Africa differed in their response to smoke or heat treatments alone or combined. Soil seed bank samples taken from 0 to 5 cm depth of the topsoil were treated with smoke-water solution, heat and heat + smoke-water combined and subsequent emergence of seedlings monitored over 90 days. In total, 790 individuals from 11 different plant families representing 37 graminoid (Poaceae) and non-graminoid species of flowering plants were identified. The most abundant plant families that emerged were Poaceae followed by Asteraceae. Grasses contributed 18% of the germinable seed bank, while non-grass (forbs and trees) species contributed >80%. The most abundant grass species that emerged was Themeda triandra and the most common forb species was Centella asiatica. Compared to the control, smoke-water (SW) and/or smoke-water + heat (H + SW) treatment resulted in a 1.6-fold increase in mean number of seedling emergence. SW and H + SW treatment of soil seed bank also resulted in fourfold to fivefold greater biomass production. These results suggest that emergence of some smoke-responsive perennial grasses (e.g. Themeda triandra) from the soil seed bank can be enhanced using smoke techniques. Moreover, plant-derived smoke could potentially have a significant role in the restoration of degraded grasslands in South Africa and elsewhere.     

Genetic population structure of <Emphasis Type="Italic">Osmunda japonica</Emphasis>, rheophilous <Emphasis Type="Italic">Osmunda lancea</Emphasis> and their hybrids

Rheophilous Osmunda lancea often hybridizes with a dryland ally, Osmunda japonica, to produce O. × intermedia, forming zonation in riverbanks and the adjacent dryland along flooding frequency clines. This study examined the genetic structure of populations consisting of O. × intermedia and the two parental species by analyzing ten nuclear DNA markers [six cleaved amplified polymorphic sequence (CAPS) markers and three simple sequence repeat (SSR) markers developed from an expressed sequence tag (EST) library, and the sequence of the glyceraldehyde-3-phosphate dehydrogenase gene GapCp] and chloroplast DNA sequences. The results suggest that the nuclear genes of O. japonica and O. lancea are genetically differentiated despite shared polymorphism in their chloroplast DNA sequences. This discrepancy may be attributable to natural selection and recent introgression, although it is not evident if introgression occurs between O. japonica and O. lancea in the examined populations. Our findings of putative F2 hybrids in O. × intermedia support its partial reproducibility, and also suggest that formation of later-generation hybrids generates morphological variation in O. × intermedia. O. lancea plants collected from geographically distant localities were genetically very similar, and it is suggested that O. lancea originated monotopically.     

Ophiostomatoid fungi can emit the bark beetle pheromone verbenone and other semiochemicals in media amended with various pine chemicals and beetle-released compounds

Fungal volatile compounds can mediate fungal-insect interactions. Whether fungi can emit insect pheromones and how volatile chemicals change in response to chemicals the fungi naturally encounter is poorly understood. We analyzed volatiles emitted by Grosmannia clavigera (symbiont of the mountain pine beetle) and Ophiostoma ips (symbiont of the pine engraver beetle) growing in liquid media amended with compounds that the fungi naturally encounter: (−)-α-pinene, (+)-α-pinene, (−)-trans-verbenol, verbenone, or ipsdienol. Nine volatile compounds were identified among the fungal and amendment treatments. Volatiles qualitatively and quantitatively differed between fungal species and among amendment treatments. The bark beetle anti-aggregation pheromone (−)-verbenone was detected from both fungi growing in (−)-trans-verbenol-amended media. G. clavigera and O. ips can emit beetle pheromones and other beetle semiochemicals, suggesting that ophiostomatoid fungi could contribute to the chemical ecology of bark beetles. However, such contributions could be modulated by the presence of other environmental chemicals.     

Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance

Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding “Plasmodium falciparum Erythrocyte Membrane Protein 1” (PfEMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.     

Clonality in South African isolates and evidence for a European origin of the root pathogen Thielaviopsis basicola

Thielaviopsis basicola is a soil-borne fungal pathogen with a wide host range and a cosmopolitan distribution. It causes disease on many agricultural crops, and in South Africa is the causal agent of black pod rot of groundnuts and black root rot on chicory. Knowledge of the population diversity of T. basicola could provide valuable information regarding management strategies, the possible movement, origin, and reproductive strategies of the fungus. The objective of this study was to determine the population diversity of T. basicola isolates from groundnuts and chicory in South Africa using co-dominant polymorphic markers. These markers were also used to compare isolates from South Africa with those from other hosts and geographic regions. Seven loci revealed nine alleles and two genotypes, one on groundnut and one on chicory, differing at only two loci. T. basicola isolates from eight different countries and ten different hosts revealed 17 genotypes across the seven loci with 39 different alleles. The lack of diversity for the two South African host-related populations of isolates suggests that T. basicola was introduced into South Africa. Some evidence is provided for a European origin of the pathogen, possibly linked to trade in root crops.     

Isolation and characterization of microsatellite loci in Ononis repens,Leguminosae

Ten polymorphic microsatellites were isolated from Ononis repens, using a microsatellite enrichment protocol and selective hybridization with a mixed synthetic dinucleotide repeat probe. Primers for DNA amplifications using polymerase chain reaction (PCR) were designed and synthesized. The loci amplified in both O. repens and O. spinosa. All 10 loci were polymorphic in each of four populations studied. These microsatellite markers will be useful for population genetic analysis and biodiversity studies of O. repens and O. spinosa.     

Antibiotic susceptibility profiles of some <Emphasis Type="Italic">Vibrio</Emphasis> strains isolated from wastewater final effluents in a rural community of the Eastern Cape Province of South Africa

Background  

To evaluate the antibiogram and antibiotic resistance genes of some Vibrio strains isolated from wastewater final effluents in a rural community of South Africa. V. vulnificus (18), V. metschnikovii (3), V. fluvialis (19) and V. parahaemolyticus (12) strains were isolated from final effluents of a wastewater treatment plant (WWTP) located in a rural community of South Africa. The disk diffusion method was used for the characterization of the antibiogram of the isolates. Polymerase chain reaction (PCR) was employed to evaluate the presence of established antibiotic resistance genes using specific primer sets.