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Previous phylogenetic analysis of ITS nrDNA sequence data for Arctotidinae species resolved a strongly supported clade containing all but one of the showy annual Arctotis species (informally designated the Arctotis Annual Clade). In the present study, phylogenetic relationships in the Arctotis Annual Clade were investigated by Bayesian inference and maximum parsimony analyses of cpDNA (trnT-trnL-trnF and trnH-psbA) and nrDNA (ITS) sequence data. The cpDNA and nrDNA phylogenies were notably incongruent. Arctotis venusta and a putative unnamed species (A. 'sp. B') were strongly supported as monophyletic by both data sets. The monophyly of A. leiocarpa was strongly supported by the ITS data set, whereas the remaining accessions formed a poorly resolved complex (the 'A. fastuosa complex'). Within the A. fastuosa complex, A. hirsuta was monophyletic with strong support in the ITS phylogeny. A statistical parsimony-derived cpDNA haplotype network resolved five broad groups of haplotypes and showed no consistent geographical structure, but species-specific haplotype lineages for A. venusta and A. sp. B were resolved. Arctotis fastuosa accessions were distributed among four haplotype groups. Incongruence between the data sets and poor resolution within the A. fastuosa complex may reflect reticulate evolution, ancestral polymorphism, and incomplete lineage sorting, in tandem with the low information content of the data sets. The greatest phenotypic diversification in the clade is in cypsela morphology. Comparison of cypsela morphology with the phylogenies suggests a general trend for reduction in the sizes of the cypsela, abaxial wings, pappus scales, and loss of pubescence during diversification. A revised taxonomy, integrating currently available evidence, accompanied by full descriptive accounts and a key to the taxa are presented. Eight species are recognized, including the nomenclatural novelties Arctotis chrysantha (sp. nov.) and Arctotis namibiensis (sp. nov.). The names Arctotis karasmontana, Venidium fugax, and Venidium macrocephalum are lectotypified. [ABSTRACT FROM AUTHOR]

This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A. sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation. [ABSTRACT FROM AUTHOR]

The dominance of a few staple crops (maize, rice, and wheat) in most agricultural systems hampers the application of interventions to improve food security and nutrition. Research and development attention has focused on improving the production and utilization of these crops, leaving other crops under‐researched and underutilized. Subsequently, there have been high malnutrition rates due to poor diet diversity, yet there are "opportunity crops" that remain under researched. The opportunity crops can unlock solutions to food insecurity, malnutrition, a lack of biodiversity, and indeed poor climate adaptation. The study explored diversification in agricultural systems to analyze whether reorientation of research investment to include under‐researched crops can increase nutrient gain and enhance dietary diversity. Research outputs benchmarked as the number of publications from three leading African universities, Nairobi, Pretoria, and Ghana, were related to crop diversity and nutrition of crops in five clusters: cereals, vegetables, legumes, roots and tubers, and nuts. The findings show that maize was the predominantly researched crop across the three institutions. Low research outputs were observed for pearl millet, finger millet, and yam across the three institutions: amaranth and nightshade (Pretoria), sweet potatoes (Pretoria and Ghana), Marama bean (Nairobi), and soya bean (Nairobi and Ghana). There was nutrient gain across all five clusters, particularly from under‐researched indigenous crops such as finger millet, amaranth, nightshade, yam, sweet potatoes, Marama bean, and soybean. Nutrient gain was contributed more by cereals and root and tuber crops from Pretoria, vegetables and nuts (Ghana), as well as legumes (Nairobi). The findings demonstrate that incorporating research on the least researched crops with successful integration of other research and development initiatives (policy and dissemination) can increase nutrition and improve dietary diversity. The nutrient gain will positively affect food security and nutrition, contributing to the achievement of Africa Agenda 2063, the United Nation's Sustainable Development Goals, and reducing food imports. The findings can inform research investment and decision across different institutions within the African continent. Research investment targeting crops such as finger millet, amaranthus, sweet potatoes, soya beans, and cashew nuts is needed considering the nutritional contribution, climate change adaptability, market potential, and biodiversity contribution. Further analysis should explore production, socio‐economic (marketability and income generation), and environmental gains (adaptive ability to climate change) for specific crops. The development of frameworks to guide the analysis of the nature and scope of factors affecting the contribution of these crops to food security and nutrition, as well as research on specific crops considering geographic distribution and institutional involvement, is also needed. [ABSTRACT FROM AUTHOR]

Chrysanthemoides monilifera Tourn. ex Medik is a noxious weed in Australia and New Zealand. It is a widespread species in southern Africa, where it shows considerable morphological variation that has resulted in a confusing infraspecific taxonomy. We use DNA sequence data from the nuclear Internal Transcribed Spacer (ITS) region from 78 samples of this species from its indigenous distribution range and 10 samples from Australia and New Zealand to determine the regions of origin of the invasive plants. These data are augmented by a smaller study using ISSR markers. Bayesian Inference analysis was somewhat resolved, with many weakly supported nodes. Clades with support tended to correspond to infraspecific taxonomic entities, and were geographically coherent. In contrast, a neighbour-net analysis was not as well resolved and indicated considerable reticulation. All analyses of ITS data retrieved two major clades corresponding to Western and Eastern distributions, with some overlap. Samples from New Zealand and Australia correspond to the taxon C. monilifera subsp. monilifera , and are resolved as most closely related to samples from the greater Cape Town area. Biological control agent populations for C. monilifera subsp. monilifera should be sourced from this region in order to avoid host plant incompatibility problems. [ABSTRACT FROM AUTHOR]

Faucaria tigrina (Haw.) Schwantes is a rare, threatened succulent found exclusively on the outskirts of Grahamstown, Eastern Cape, South Africa. There are three extant populations of the species; two large ones (approximately 300 and 620 adults) separated by under two kilometres, and a third very much smaller one slightly further away. Genetic theory expects that smaller, isolated populations face a loss in genetic variation through inbreeding and genetic drift and that as declining genetic variation is linked to a loss in fitness, this species may face extinction in the long term. This study used the ISSR-PCR genetic methods linked to an automated detection platform to determine if these populations are genetically distinct, and whether they are genetically depauperate. Two ISSR primers were used, and the automated detection system identified a total of 572 ISSR loci. An UPGMA clustering analysis showed each population to be genetically distinct, and that the genetic diversity of each population does not appear to be particularly low. F. tigrina is separable from the related Faucaria britteniae L. Bolus using the ISSR method, suggesting that this method may be appropriate for systematic studies in the Aizoaceae, which comprises many genera with closely related species. [ABSTRACT FROM AUTHOR]

Background and Aims The ability of plant lineages to reach all continents contributes substantially to their evolutionary success. This is exemplified by the Poaceae, one of the most successful angiosperm families, in which most higher taxa (tribes, subfamilies) have global distributions. Due to the old age of the ocean basins relative to the major angiosperm radiations, this is only possible by means of long-distance dispersal (LDD), yet the attributes of lineages with successful LDD remain obscure. Polyploid species are over-represented in invasive floras and in the previously glaciated Arctic regions, and often have wider ecological tolerances than diploids; thus polyploidy is a candidate attribute of successful LDD. Methods The link between polyploidy and LDD was explored in the globally distributed grass subfamily Danthonioideae. An almost completely sampled and well-resolved species-level phylogeny of the danthonioids was used, and the available cytological information was assembled. The cytological evolution in the clade was inferred using maximum likelihood (ML) as implemented in ChromEvol. The biogeographical evolution in the clade was reconstructed using ML and Bayesian approaches. Key Results Numerous increases in ploidy level are demonstrated. A Late Miocene–Pliocene cycle of polyploidy is associated with LDD, and in two cases (the Australian Rytidosperma and the American Danthonia) led to secondary polyploidy. While it is demonstrated that successful LDD is more likely in polyploid than in diploid lineages, a link between polyploidization events and LDD is not demonstrated. Conclusions The results suggest that polyploids are more successful at LDD than diploids, and that the frequent polyploidy in the grasses might have facilitated the extensive dispersal among continents in the family, thus contributing to their evolutionary success. [ABSTRACT FROM PUBLISHER]

The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300–4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid-Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models. © The Willi Hennig Society 2009. [ABSTRACT FROM AUTHOR]

Aim The genus Kniphofia contains 71 species with an African–Malagasy distribution, including one species from Yemen. The genus has a general Afromontane distribution. Here we explore whether Kniphofia is a floristic indicator of the Afromontane centre of endemism and diversity. The South Africa Centre of diversity and endemism was explored in greater detail to understand biogeographical patterns. Location Africa, Afromontane Region, southern Africa, Madagascar and Yemen. Methods Diversity and endemism for the genus were examined at the continental scale using a chorological approach. Biogeographical patterns and endemism in the South Africa Centre were examined in greater detail using chorology, phenetics, parsimony analysis of endemicity (PAE) and mapping of range-restricted taxa. Results Six centres of diversity were recovered, five of which are also centres of endemism. Eight subcentres of diversity are proposed, of which only two are considered subcentres of endemism. The South Africa Centre is the most species-rich region and the largest centre of endemism for Kniphofia. The phenetic analysis of the South Africa Centre at the full degree square scale recovered three biogeographical areas that correspond with the subcentres obtained from the chorological analysis. The PAE (at the full degree square scale) and the mapping of range-restricted taxa recovered two and six areas of endemism (AOEs), respectively. These latter two approaches produced results of limited value, possibly as a result of inadequate collecting of Kniphofia species. Only two AOEs were identified by PAE and these are embedded within two of the six AOEs recovered by the mapping of range-restricted taxa. All the above AOEs are within the three subcentres found by chorological and phenetic analysis (at the full degree square scale) for the South Africa Centre. Main conclusions The centres for Kniphofia broadly correspond to the Afromontane regional mountain systems, but with some notable differences. We regard Kniphofia as a floristic indicator of the Afromontane Region sensu lato. In southern Africa, the phenetic approach at the full-degree scale retrieved areas that correlate well with those obtained by the chorological approach. [ABSTRACT FROM AUTHOR]

Abstract: The majority of the approximately 80–90 species in subtribe Arctotidinae occur in southern Africa with the centre of diversity in the winter-rainfall region. Three species are restricted to afromontane eastern Africa and three species are endemic to Australia. To investigate biogeographic and phylogenetic relationships within Arctotidinae, sequence data from four cpDNA regions (psbA-trnH, trnT-trnL and trnL-trnF spacers and trnL intron) and the ITS nrDNA region for 59 Arctotidinae species were analyzed with parsimony and Bayesian-inference approaches. Eight well-supported major lineages were resolved. The earliest-diverging extant lineages are afromontane or inhabit mesic habitats, whereas almost all sampled taxa from the winter-rainfall and semi-arid areas have diverged more recently. Molecular dating estimated that the major clades diverged during the Miocene and Pliocene, which is coincident with the trend of increasing rainfall seasonality, aridification and vegetation changes in southwestern Africa. Trans-oceanic dispersal to Australia was estimated to have occurred during the Pliocene. [Copyright &y& Elsevier]

Abstract: This study constitutes the first evolutionary investigation of the snake family Psammophiidae—the most widespread, most clearly defined, yet perhaps the taxonomically most problematic of Africa’s family-level snake lineages. Little is known of psammophiid evolutionary relationships, and the type genus Psammophis is one of the largest and taxonomically most complex of the African snake genera. Our aims were to reconstruct psammophiid phylogenetic relationships and to improve characterisation of species boundaries in problematic Psammophis species complexes. We used approximately 2500 bases of DNA sequence from the mitochondrial and nuclear genomes, and 114 terminals covering all psammophiid genera and incorporating approximately 75% of recognised species and subspecies. Phylogenetic reconstructions were conducted primarily in a Bayesian framework and we used the Wiens/Penkrot protocol to aid species delimitation. Rhamphiophis is diphyletic, with Rhamphiophis acutus emerging sister to Psammophylax. Consequently we transfer the three subspecies of Rhamphiophis acutus to the genus Psammophylax. The monotypic genus Dipsina is sister to Psammophis. The two species of Dromophis occupy divergent positions deeply nested within Psammophis, and we therefore relegate Dromophis to the synonymy of Psammophis. Our results allow division of the taxonomically problematic Psammophis ‘sibilans’ species complex into two monophyletic entities, provisionally named the ‘phillipsii’ and ‘subtaeniatus’ complexes. Within these two clades we found support for the status of many existing species, but not for a distinction between P.p. phillipsii and P. mossambicus. Additionally, P. cf. phillipsii occidentalis deserves species status as the sister taxon of P. brevirostris. [Copyright &y& Elsevier]

Aim The flowering plant family Proteaceae is putatively of Gondwanan age, with modern and fossil lineages found on all southern continents. Here we test whether the present distribution of Proteaceae can be explained by vicariance caused by the break-up of Gondwana. Location Africa, especially southern Africa, Australia, New Zealand, South America, New Caledonia, New Guinea, Southeast Asia, Sulawesi, Tasmania. Methods We obtained chloroplast DNA sequence data from the rbcL gene, the rbcL- atpB spacer, and the atpB gene from leaf samples of forty-five genera collected from the field and from living collections. We analysed these data using Bayesian phylogenetic and molecular dating methods, with five carefully selected fossil calibration points to obtain age estimates for the nodes within the family. Results Four of eight trans-continental disjunctions of sister groups within our sample of the Proteaceae post-date the break-up of Gondwana. These involve independent lineages, two with an Africa-Australia disjunction, one with an Africa–South America disjunction, and one with a New Zealand–Australasia disjunction. The date of the radiation of the bird-pollinated Embothriinae corresponds approximately to the hypothesized date of origin of nectar-feeding birds in Australia. Main conclusions The findings suggest that disjunct distributions in Proteaceae result from both Gondwanan vicariance and transoceanic dispersal. Our results imply that ancestors of some taxa dispersed across oceans rather than rafting with Gondwanan fragments as previously thought. This finding agrees with other studies of Gondwanan plants in dating the divergence of Australian, New Zealand and New Caledonian taxa in the Eocene, consistent with the existence of a shared, ancestral Eocene flora but contrary to a vicariance scenario based on accepted geological knowledge. [ABSTRACT FROM AUTHOR]

Leucadendron is a moderately large genus of Proteaceae almost entirely restricted to the Cape Floristic Region of southern Africa. The genus is unusual in being dioecious and sexually dimorphic. ITS sequence data were obtained from 62 of the 96 currently recognized taxa (85 species and 11 subspecies). Phylogenetic analyses were conducted under Maximum Likelihood and parsimony and resolved nine groups of species with varying degrees of bootstrap support, but relationships between these groups are largely unsupported. The phylogeny conflicts with the current taxonomic arrangement, which is based mainly on fruit morphology. The two sections of the genus, Alatosperma and Leucadendron, and several subsections within these sections, are resolved as non-monophyletic. This means that taxonomically important characters (such as fruit shape) have evolved multiple times, as the species with nut-like fruit (resolved into two of the nine groups) appear to have evolved independently from ancestors with winged fruit. Based on the topology obtained, the life history traits of anemophily, myrmechochory, and re-sprouting have also originated multiple times. Dispersal–Vicariance (DIVA) analysis suggests that the genus had an ancestral area in the Karoo Mountain and Southeastern phytogeographic centres of endemism in the southwestern Cape. [Copyright &y& Elsevier]

Phylogenetic relationships among advanced snakes ( Acrochordus + Colubroidea = Caenophidia) and the position of the genus Acrochordus relative to colubroid taxa are contentious. These concerns were investigated by phylogenetic analysis of fragments from four mitochondrial genes representing 62 caenophidian genera and 5 noncaenophidian taxa. Four methods of phylogeny reconstruction were applied: matrix representation with parsimony (MRP) supertree consensus, maximum parsimony, maximum likelihood, and Bayesian analysis. Because of incomplete sampling, extensive missing data were inherent in this study. Analyses of individual genes retrieved roughly the same clades, but branching order varied greatly between gene trees, and nodal support was poor. Trees generated from combined data sets using maximum parsimony, maximum likelihood, and Bayesian analysis had medium to low nodal support but were largely congruent with each other and with MRP supertrees. Conclusions about caenophidian relationships were based on these combined analyses. The Xenoderminae, Viperidae, Pareatinae, Psammophiinae, Pseudoxyrophiinae, Homalopsinae, Natricinae, Xenodontinae, and Colubrinae (redefined) emerged as monophyletic, whereas Lamprophiinae, Atractaspididae, and Elapidae were not in one or more topologies. A clade comprising Acrochordus and Xenoderminae branched closest to the root, and when Acrochordus was assessed in relation to a colubroid subsample and all five noncaenophidians, it remained associated with the Colubroidea. Thus, Acrochordus + Xenoderminae appears to be the sister group to the Colubroidea, and Xenoderminae should be excluded from Colubroidea. Within Colubroidea, Viperidae was the most basal clade. Other relationships appearing in all final topologies were (1) a clade comprising Psammophiinae, Lamprophiinae, Atractaspididae, Pseudoxyrophiinae, and Elapidae, within which the latter four taxa formed a subclade, and (2) a clade comprising Colubrinae, Natricinae, and... [ABSTRACT FROM AUTHOR]

Keywords: biodiversity; community ecology; conservation; environmental drivers; fragmentation; Southern Africa; species richness EN biodiversity community ecology conservation environmental drivers fragmentation Southern Africa species richness 784 787 4 09/02/22 20220901 NES 220901 INTRODUCTION Anthropogenic habitat modification is the single biggest cause of forest habitat loss (Alroy, 2017; Ewers & Didham, 2006; Fahrig, 2003). Thus, investigating the small mammal populations in South African forests is an important first step to understanding the effects of forest fragmentation on forest fauna (Lindenmayer et al., 2002). Patch occupancy and potential metapopulation dynamics of three forest mammals in fragmented Afromontane forests in South Africa. Four species were caught across the nine forest patches; I Michaelamys namaquensis i (Namaqua rock mouse), I Myosorex varius i (forest shrew) I Graphiurus murinus i (woodland dormouse) and I Mastomys natalensis senu lato i (multimammate mouse) (Table 2). [Extracted from the article]

Features a study which examined the morphological variation within the plant species Merxmuellera cincta to test for the existence of discreet taxonomic entity. Phenetic study of Merxmuellera cincta; Cytology of the species; Results and discussion.

Some plant species possess structures known as leaf domatia, which house mites. The association between domatia-bearing plants and mites has been proposed to be mutualistic, and has been found to be important in species of economic value, such as grapes, cotton, avocado and coffee. This is because leaf domatia affect the distribution, diversity and abundance of predatory and mycophagous mites found on the leaf surface. As a result, plants are thought to benefit from increased defence against pathogens and small arthropod herbivores. This study assesses the relative diversity and composition of mites on an economically important plant host (Coffea aribica) in comparison to mites found in a neighbouring indigenous forest in South Africa. Our results showed that the coffee plantations were associated with only predatory mites, some of which are indigenous to South Africa. This indicates that coffee plantations are able to be successfully colonised by indigenous beneficial mites. We also found an "edge effect", in that coffee trees at the edge of the plantation hosted fewer mite species. These results are a snap-shot from a single sampling period. Nonetheless, they highlight the potential importance of this mutualism in commercial crop species and the possible role of faunal exchanges between indigenous and exotic crop species. This study expands our understanding of the mite–plant mutualism in Southern Africa, a region where acarological studies are sparse. [ABSTRACT FROM AUTHOR]

The article presents a discussion on the moss flora of southern South Africa. Although comparatively not as diverse and unique as the vascular flora that comprises about 23404 species, 80% of which are endemic, the moss flora of southern Africa includes over 570 moss species. The moss flora of southern Africa thus includes about 6% of the species in the world and a significant number of endemics. Although southern Africa is probably one of the best known African regions bryologically, and one of the few with its own comprehensive moss flora, the size of this huge territory makes it challenging to explore. Several new species and mosses new to Africa have been recorded.

A new phytoseiids species, Typhlodromus (Anthoseius) uhoneae sp.n. is described from plants with domatia. In addition, 8 known phytoseiid species also associated with plants with domatia are discussed. A key to all the South African species of the subgenus Anthoseius is given. [ABSTRACT FROM AUTHOR]

The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four‐gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa. The tribe appears to have diversified during the Cenozoic, beginning c. 50–32 Ma, with most extant African lineages originating in the Miocene or later, well after the breakup of the Gondwanan landmass. Biogeographical analysis suggests an African origin for the tribe and a single dispersal event founding the Asian platypleurines, although additional taxon sampling and genetic data will be needed to confirm this pattern because key nodes in the tree are still weakly supported. Two Platypleurini genera from Madagascar (Pycna Amyot & Audinet‐Serville, Yanga Distant) are found to have originated by late Miocene dispersal of a single lineage from Africa. The genus Platypleura is recovered as polyphyletic, with Platypleura signifera Walker from South Africa and many Asian/Indian species apparently requiring assignment to different genera, and a new Platypleura concept is proposed with the synonymization of Azanicada Villet syn.n. The genera Orapa Distant and Hamza Distant, currently listed within separate tribes but suspected of platypleurine affinity, are nested deeply within the Platypleurini radiation. The tribe Orapini syn.n. is here synonymized while the tribe Hamzini is pending a decision of the ICZN to preserve nomenclatorial stability. [ABSTRACT FROM AUTHOR]

The influence of fire regimes on soil microbial diversity in montane grasslands is a relatively unexplored area of interest. Understanding the belowground diversity is a crucial stepping-stone toward unravelling community dynamics, nutrient sequestration, and overall ecosystem stability. In this study, metabarcoding was used to unravel the impact of fire disturbance regimes on bacterial and arbuscular mycorrhizal fungal community structures in South African montane grasslands that have been subjected to an intermediate (up to five years) term experimental fire-return interval gradient. Bacterial communities in this study exhibited a shift in composition in soils subjected to annual and biennial fires compared to the controls, with carbon and nitrogen identified as significant potential chemical drivers of bacterial communities. Shifts in relative abundances of dominant fungal operational taxonomic units were noted, with Glomeromycota as the dominant arbuscular mycorrhiza observed across the fire-return gradient. A reduction in mycorrhizal root colonisation was also observed in frequently burnt autumnal grassland plots in this study. Furthermore, evidence of significant mutualistic interactions between bacteria and fungi that may act as drivers of the observed community structure were detected. Through this pilot study, we can show that fire regime strongly impacts bacterial and fungal communities in southern African montane grasslands, and that changes to their usually resilient structure are mediated by seasonal burn patterns, chemical drivers, and mutualistic interactions between these two groups. [ABSTRACT FROM AUTHOR]

Two new species of Indigofera L. (Leguminosae) are described from the Sneeuberg Centre of Floristic Endemism on the southern Great Escarpment, Eastern and Western Cape Provinces, South Africa. Both species are localised high-altitude endemics. Indigofera magnifica Schrire & V.R. Clark is confined to the summit plateau of the Toorberg--Koudeveldberg--Meelberg west of Graaff-Reinet, and complements other western Sneeuberg endemics such as Erica passerinoides (Bolus) E.G.H. Oliv. and Faurea recondita Rourke & V.R. Clark. Indigofera asantasanensis Schrire & V.R. Clark is confined to a small area east of Graaff-Reinet, and complements several other eastern Sneeuberg endemics such as Euryops exsudans B. Nord & V.R. Clark and E. proteoides B. Nord. & V.R. Clark. Based on morphology, both new species belong to the Cape Clade of Indigofera, supporting a biogeographical link between the Cape Floristic Region and the Sneeuberg, as well as with the rest of the eastern Great Escarpment. [ABSTRACT FROM AUTHOR]

Aim Based on mitochondrial DNA (mt DNA) data, many organisms with ranges spanning multiple biogeographical regions exhibit genetic structure across the transition zones between these regions, while others appear to be genetically homogenous. No clear link has been found between the presence or absence of such spatial genetic discontinuities and species' dispersal potential, confounding the formulation of general predictions concerning genetic structure. The fact that discrepancies between mt DNA and nuclear markers are common across semi-permeable barriers suggests that a lack of structure could be attributable to mt DNA-specific properties of inheritance. We re-examined genetic structure in the coastal crab Hymenosoma orbiculare, a species that is represented by a single mt DNA lineage across the Atlantic/Indian Ocean biogeographical transition zone, by comparing mt DNA data with nuclear DNA data. Location South Africa's cool-temperate and warm-temperate marine biogeographical provinces. Methods DNA sequence data from the mitochondrial COI gene and the intron of the nuclear ANT gene were generated for 150 individuals of H. orbiculare. For each locus, we determined whether the sharing of alleles between provinces was the result of either the retention of ancestral polymorphism or of secondary contact. Results We recovered two nuclear intron lineages whose spatial genetic structure reflects contemporary biogeographical and oceanographical conditions, indicating that the existence of a single mt DNA lineage is not a function of unexpectedly high levels of dispersal. Main conclusions Mt DNA-based genetic homogeneity is increasingly being reported in coastal organisms with ranges spanning biogeographical transition zones that define distinct evolutionary lineages in other species. Our results stress the importance of revisiting single-locus data sets by means of multilocus genetic approaches before any conclusions can be drawn about the role of biogeographical transition zones in driving genetic structure. [ABSTRACT FROM AUTHOR]

Baits or lures are commonly used for surveying small mammal communities, not only because they attract large numbers of these animals, but also because they provide sustenance for trapped individuals. In this study we used Sherman live traps with five bait treatments to sample small mammal populations at three high-altitude sites (>1700 m) in the Sneeuberg Mountain Complex of the Eastern Cape Province, South Africa.We investigated the influence of bait treatment on three parameters commonly recorded in small mammal surveys. In addition, we investigated how different bait treatments vary in measuring species richness using the Chao 2 species richness estimator together with rarefaction curves. Overall, 12 small mammal species were sampled. A combination of birdseed and banana captured the highest number of species (11) but the most successful bait overall was peanut butter and oats (greatest number of captures, recaptures, number of individuals and highest Shannon diversity). The Chao 2 richness estimator indicated that four of the five bait treatments reached their sampling capacity. Rarefaction curves indicated that all bait treatments are similar with regard to species accumulation. This could possibly be explained by odours left behind in traps as even un-baited traps (i.e. controls) captured seven different small mammal species. We conclude that the most suitable bait for surveying small mammals at high altitude in South Africa is peanut butter and oats. However, using peanut butter and oats in combination with other bait treatments will improve estimates of diversity when surveying small mammal communities. [ABSTRACT FROM AUTHOR]

Background: When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. Results: We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. Conclusions: This is the first study to report sex-specific differences in genetic structure based on matrilineallyinherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation. [ABSTRACT FROM AUTHOR]

* Premise: The cosmopolitan and ecologically important grass subfamily Aristidoideae comprises the widely distributed genus Aristida (250-290 species), Stipagrostis (50 species, with an African-Asian distribution), and Sartidia (five species, Africa and Madagascar). The subfamily includes species with C3 (Sartidia and a single species of Aristida) and C4 photosynthetic pathways. Rigorous phylogenetic reconstructions of species relationships are required to explain the biogeographic, physiological, and ecological diversity within this subfamily. * Methods: Chloroplast (trnL-F, rpl16) and nuclear (ITS) DNA sequences were obtained from 198 accessions, and the combined data set was subjected to parsimony, maximum likelihood, and Bayesian inference analyses. Dating analyses calibrated using previously published node ages were conducted to determine the ages of major radiations. * Results: The C3 Sartidia is sister to a monophyletic Stipagrostis, and the (Sartidia, Stipagrostis) clade is sister to Aristida. Within Aristida, the only known C3 species, A. longifolia, is sister to the remainder of the genus. Infrageneric sections of Aristida were not supported, and there are no synapomorphic morphological characters for the clades retrieved. Within Aristida, monophyletic Australian, African, North American, and South American clades are retrieved. * Conclusions: The subfamily dates back to the late Miocene, with the major lineages present by the Pliocene. With one exception, regional clades of Aristida evolved in the Pliocene. The C3 photosynthetic pathway is hypothesized to be the pleisomorphic condition for the subfamily, wherein two independent C4 pathways (each with unique anatomical and genetic features) evolved, one within Aristida and one in Stipagrostis. [ABSTRACT FROM AUTHOR]

A new species of Psoralea is described. Psoralea margaretiflora C.H. Stirton & V.R. Clark is endemic to the Sneeuberg Centre of Floristic Endemism, Eastern Cape, South Africa. This resprouter is characterised by its small greenish-white flowers with a small trifid purple nectar patch and translucent veins; 5(-7)-pinnate leaflets; multi-branching erect short seasonal flowering shoots; and tall habit of many stiff bare stems with the seasonal shoots massed at the apex. It is most similar to P. oligophylla Eckl. & Zeyh., a widespread species found in the Eastern Cape. The reseeder P. oligophylla differs in its lax virgate spreading habit with numerous long glaucous seasonal shoots; single stem, 1(-3)- glaucous leaflets; more numerous white flowers; and standard petals with a purple ring surrounding a bright yellow nectar patch. [ABSTRACT FROM AUTHOR]

A new species of Psoralea is described. Psoralea margaretiflora C.H. Stirton & V.R. Clark is endemic to the Sneeuberg Centre of Floristic Endemism, Eastern Cape, South Africa. his resprouter is characterised by its small greenish-white flowers with a small trifid purple nectar patch and translucent veins; 5(-7)-pinnate leaflets; multi-branching erect short seasonal flowering shoots; and tall habit of many stiff bare stems with the seasonal shoots massed at the apex. It is most similar to P. oligophylla Eckl. & Zeyh., a widespread species found in the Eastern Cape. The reseeder P. oligophylla differs in its lax virgate spreading habit with numerous long glaucous seasonal shoots; single stem, 1(-3)- glaucous leaflets; more numerous white flowers; and standard petals with a purple ring surrounding a bright yellow nectar patch. [ABSTRACT FROM AUTHOR]

Schotia has a southern African distribution with a strong affinity to the thicket biome and is a potential indicator of thicket biogeography. This study uses DNA sequence data (from the chloroplast and nuclear genomes) to infer interspecific phylogenetic relationships, to elucidate the evolutionary history of Schotia, and to extrapolate findings to the history of the thicket biome. Four species of Schotia represented by multiple samples were nonmonophyletic for both chloroplast and nuclear markers. These results may be due to hybridization and/or incomplete lineage sorting, which also suggests a recent origin of Schotia morphospecies. The center of genetic and taxonomic diversity of Schotia is the Eastern Cape and partly the Western Cape, coinciding with the hub of present-day thicket distribution. This region is hypothesized as being a refugial area for Schotia (and the associated thicket biome) during glacial periods, with expansion beyond this region during interglacial periods. [ABSTRACT FROM AUTHOR]

We explore the potential impact of conflicting gene trees on inferences of evolutionary history above the species level. When conflict between gene trees is discovered, it is common practice either to analyze the data separately or to combine the data having excluded the conflicting taxa or data partitions for those taxa (which are then recoded as missing). We demonstrate an alternative approach, which involves duplicating conflicting taxa in the matrix, such that each duplicate is represented by one partition only. This allows the combination of all available data in standard phylogenetic analyses, despite reticulations. We show how interpretation of contradictory gene trees can lead to conflicting inferences of both morphological evolution and biogeographic history, using the example of the pampas grasses, Cortaderia. The characteristic morphological syndrome of Cortaderia can be inferred as having arisen multiple times (chloroplast DNA [cpDNA]) or just once (nuclear ribosomal DNA [nrDNA]). The distributions of species of Cortaderia and related genera in Australia/New Guinea, New Zealand, and South America can be explained by few (nrDNA) or several (cpDNA) dispersals between the southern continents. These contradictions can be explained by past hybridization events, which have linked gains of complex morphologies with unrelated chloroplast lineages and have erased evidence of dispersals from the nuclear genome. Given the discrepancies between inferences based on the gene trees individually, we urge the use of approaches such as ours that take multiple gene trees into account. [ABSTRACT FROM PUBLISHER]

Abstract: The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region biodiversity hotspot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this diversity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints, reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to diversify in the Cape only 5–18Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to diversify in the Cape 22–39Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region. [Copyright &y& Elsevier]

This analysis goes beyond many phylogenies in exploring how phylogenetic structure imposed by morphology, ecology, and geography reveals useful evolutionary data. A comprehensive range of such diversity is evaluated within tribe lndigofereae and outgroups from sister tribes. A combined data set of 321 taxa (over one-third of the tribe) by 80 morphological characters, 833 aligned nuclear ribosomal !TS/5.8S sites, and an indel data set of 33 characters was subjected to parsimony analysis. Notable results include the Madagascan dry forest Disynstemon resolved as sister to tribe lndigofereae, and a!! species of the large genus Indigofera comprise just four main clades, each diagnosable by morphological synapomorphies and ecological and geographical predilections. These results suggest niche conservation (ecology) and dispersal limitation (geography) are important processes rendering signature shapes to the lndigofereae phylogeny in different biomes. Clades confined to temperate and succulent-rich biomes are more dispersal limited and have more geographical phylogenetic structure than those inhabiting tropical grass-rich vegetation. The African arid corridor, particularly the Namib center of endemism, harbors many of the oldest Indigofera lineages. A rates analysis of nucleotide substitutions confirms that the ages of the oldest crown clades are mostly younger than 16 Ma, implicating dispersal in explaining the worldwide distribution of the tribe. [ABSTRACT FROM AUTHOR]

Arctotis debensis R.J.McKenzie, a new species from the Albany Centre of Floristic Endemism, South Africa, is described and illustrated. It grows almost exclusively in grassland on kommetjies, a distinctive landform of depressions and mounds associated with giant earthworms, in a restricted area west of King William’s Town, Eastern Cape Province. It is the first plant taxon reported to be endemic or near-endemic to this unusual habitat. The new species appears to have been collected rarely and previous collections examined have remained undetermined to species level. The new species is distinguished from closely allied species by the combination of its usually larger dimensions in all parts, prostrate habit, coriaceous leaves that are green, scabrous, and eglandular on the adaxial surface and densely lanate on the abaxial surface, and involucral-bract morphology. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 151, 581–588. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett's ice rat, Otomys sloggetti , and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment). [ABSTRACT FROM AUTHOR]

South Africa's 800 km-long southern Great Escarpment hosts numerous endemic plant species only known from their type specimens or from very few records. This is a legacy of a 100-150 year lag between the pioneer work of 19th century botanists and repeat fieldwork in the 21st century. As a result, population and ecological data are lacking for many local endemic species. Here we report on the rediscovery of Lotononis harveyi B.-E.van Wyk 147 years after its original description, and provide the first detailed ecological notes on the poorly known shrub Macowania revoluta Oliv. Both species are locally endemic to the Great Winterberg-Amatholes (Eastern Cape Province). With only six known individuals, L. harveyi is recommended the conservation status of Critically Endangered, with fire (and potentially grazing) being the main population constraints. Macowania revoluta is locally abundant, and it is surprising that it has been so poorly collected in recent decades. It occupies an important local niche as a keystone montane wetland species, and its narrow distribution range -- combined with pressure from woody alien invasive species -- suggests that its conservation status should be Rare. The research further highlights the need for continued biodiversity field research along South Africa's poorly explored Great Escarpment. [ABSTRACT FROM AUTHOR]

The article presents the geographical patterning found in the southern African danthonioid grass species, Tenaxia disticha. Topics covered include the four varieties discriminated and recognized, the distribution and localization, and haplotypes. It mentions the Drakensberg varieties, phylogeographical model, and the examination of anatomical variation of the species. Also explored is the cause of the sub-alpine climate.

The article presents a study on the morphology of Albuca (A.) bifolia or Baker. The study involves an extensive field work on the revision of the genus Albuca L. in Grahamstown, South Africa. The result shows that Albuca anisocrispa and A. pseudobifolia are closely related to A. bifolia in terms of floral, vegetative, chronological, and ecological data.

Background: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa. Results: Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya). Conclusions: The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review. [ABSTRACT FROM AUTHOR]

Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets ( Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis. Although phylogeographic breaks were present in two species, how these became established differed depending on their life histories. In the direct developer, lack of gene flow following divergence, and demographic expansion from a small initial size in the species' subtropical population, point to a single colonisation event. In contrast, the evolutionary lineages of the planktonic disperser split into two genetic lineages with much larger initial population sizes and southward gene flow continued at least periodically, indicating that divergence in this species may have been driven by a combination of reduced larval dispersal and divergent selection. These findings help explain why the presence or absence of phylogeographic breaks often appears to be independent of species' dispersal potential. [ABSTRACT FROM AUTHOR]

Albuca tenuifolia Baker was described and illustrated in 1872 from South African material sent by Peter MacOwan to William Wilson Saunders in England, without a precise locality. Since then this species has been cited in later works although with many uncertainties. In addition, no type has been designated for this taxon. After field work in the Great Escarpment in South Africa, some populations of A. tenuifolia have been rediscovered growing in rocky places at high altitude. Data on morphology, ecology, and distribution are reported, and a lectotype and epitype are designated to fix the use of the name. Affinities with other species are also discussed. [ABSTRACT FROM AUTHOR]

The name Albuca caudata Jacq. has been widely misunderstood or even ignored since its description in 1791. After studying herbarium specimens and living populations in South Africa, plants fitting Jacquin's concept of that species are found to be widely distributed in the Eastern Cape, mainly in the Albany centre of Endemism. Furthermore, some divergent specimens matching Baker's concept of A. caudata are described as a new related species: A. bakeri. Data on typification, morphology, ecology, and distribution are reported for both taxa. Affinities and divergences with other close allies are also discussed. [ABSTRACT FROM AUTHOR]

The two fuliginous albatross species, Phoebetria fusca (the Sooty albatross, SA) and P. palpebrata (the Light-mantled albatross, LMA), are found breeding close to each other on the Prince Edward Islands (Southern Ocean). Adults of these two species are easy to identify in the field, but the chicks are difficult to distinguish on the basis of external morphology, especially at very young ages. Many ecological studies involve sampling of chicks as well as adults, and accurate field identification of chicks is thus crucial. Traditionally, the extent of the ring of pale feathers around the eye (eye-ring) has been used to identify the fledglings. The aim of our study was to investigate the utility of characters associated with the eye-ring (extent, measured as an angle, and colour) for the identification of Phoebetria chicks. This was achieved by comparison of identifications based on morphology, with positive identifications based on DNA sequence data from the mitochondrial cytochrome b gene. We confirm the value of morphological criteria in distinguishing LMA and SA chicks, and this technique appears to be accurate in the majority of cases (>80%). However, we recommend using molecular identification for borderline cases (angle of the eye-ring measuring between 85 and 95°) if independent confirmation of chick identity cannot be obtained (e.g. via observed feeding interaction with an adult). [ABSTRACT FROM AUTHOR]

The southern African marine realm is located at the transition zone between the Atlantic and Indo-Pacific biomes. Its biodiversity is particularly rich and comprises faunal and floral elements from the two major oceanic regions, as well as a large number of endemics. Within this realm, strikingly different biota occur in close geographic proximity to each other, and many of the species with distributions spanning two or more of the region's marine biogeographic provinces are divided into evolutionary units that can often only be distinguished on the basis of genetic data. In this review, we describe the state of marine phylogeography in southern Africa, that is, the study of evolutionary relationships at the species level, or amongst closely related species, in relation to the region's marine environment. We focus particularly on coastal phylogeography, where much progress has recently been made in identifying phylogeographic breaks and explaining how they originated and are maintained. We also highlight numerous shortcomings that should be addressed in the near future. These include: the limited data available for commercially important organisms, particularly offshore species; the paucity of oceanographic data for nearshore areas; a dearth of studies based on multilocus data; and the fact that studying the role of diversifying selection in speciation has been limited to physiological approaches to the exclusion of genetics. It is becoming apparent that the southern African marine realm is one of the world's most interesting environments in which to study the evolutionary processes that shape not only regional, but also global patterns of marine biodiversity. [ABSTRACT FROM AUTHOR]

The name Albuca caudata Jacq. has been widely misunderstood or even ignored since its description in 1791. After studying herbarium specimens and living populations in South Africa, plants fitting Jacquin's concept of that species are found to be widely distributed in the Eastern Cape, mainly in the Albany centre of Endemism. Furthermore, some divergent specimens matching Baker's concept of A. caudata are described as a new related species: A. bakeri. Data on typification, morphology, ecology, and distribution are reported for both taxa. Affinities and divergences with other close allies are also discussed. [ABSTRACT FROM AUTHOR]

The first empirically supported phylogenetic hypothesis of relationships for the southern African endemic butterfly tribe Dirini is presented. Data derived from the morphology and ecology of the adults and immature stages (33 characters), and portions of the mitochondrial gene cytochrome oxidase I ( COI) and the nuclear genes elongation factor 1α ( EF1α) and wingless ( WG) (totalling 1734 bp) were used to infer the relationships of the in-group genera. An expanded molecular dataset using four genera from the Nymphalini and Satyrini to root the tree, and three genera from the Melanitini to test the monophyly of the tribe, was analysed using parsimony and Bayesian methods. Estimates of divergence times were calculated using two fossil calibrations under a relaxed molecular clock model. The monophyly of the tribe and each in-group genus were strongly supported. Key findings are the sister-taxon relationship of Aeropetes and Tarsocera, the apparent simultaneous or nearly simultaneous radiation of four lineages, the polyphyly of the species within Torynesis, and the apparent trans-Atlantic dispersal of the ancestors of Manataria about 40 Ma. Estimates of divergence times indicate that the tribe has undergone two major radiations since its origin: the first when they left forest habitats in the mid-late Oligocene, shortly after the radiation of the grasses (Poaceae), and the second in the early-middle Pliocene, coinciding with the aridification of southern Africa and the spread of conditions that favoured C grasses over the C grasses that dirine larvae prefer to eat. The high species diversity within the tribe appears to be partly a taxonomic artefact that may have resulted from the misinterpretation of climate-related phenotypic variation within extant species. Relocation and breeding experiments should test this hypothesis. [ABSTRACT FROM AUTHOR]

Abstract: The snake family Lamprophiidae Fitzinger (Serpentes: Elapoidea) is a putatively Late Eocene radiation of nocturnal snakes endemic to the African continent. It incorporates many of the most characteristic and prolific of Africa’s non-venomous snake species, including the widespread type genus Lamprophis Fitzinger, 1843 (house snakes). We used approximately 2500 bases of mitochondrial and nuclear DNA sequence data from 28 (41%) of the approximately 68 recognised lamprophiid species in nine of the eleven genera to investigate phylogenetic structure in the family and to inform taxonomy at the generic level. Cytochrome b, ND4 and tRNA gene sequences (mitochondrial) and c-mos sequences (nuclear) were analysed using Maximum Likelihood, Bayesian Inference and Maximum Parsimony methods. The genus Mehelya Csiki, 1903 was paraphyletic with respect to Gonionotophis Boulenger, 1893. To address this, the concept of Gonionotophis is expanded to include all current Mehelya species. The genus Lamprophis emerged polyphyletic: the enigmatic Lamprophis swazicus was sister to Hormonotus modestus from West Africa, and not closely related to its nominal congeners. It is moved to a new monotypic genus (Inyoka gen. nov.). The remaining Lamprophis species occur in three early-diverging lineages. (1) Lamprophis virgatus and the widely distributed Lamprophis fuliginosus species complex (which also includes Lamprophis lineatus and Lamprophis olivaceus) formed a clade for which the generic name Boaedon Duméril, Bibron & Duméril, 1854 is resurrected. (2) The water snakes (Lycodonomorphus) were nested within Lamprophis (sensu lato), sister to Lamprophis inornatus. We transfer this species to the genus Lycodonomorphus Fitzinger, 1843. (3) We restrict Lamprophis (sensu strictissimo) to a small clade of four species endemic to southern Africa: the type species of Lamprophis Fitzinger, 1843 (Lamprophis aurora) plus Lamprophis fiskii, Lamprophis fuscus and Lamprophis guttatus. [Copyright &y& Elsevier]

Background: Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit. Results: Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate. Conclusions: This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the source region of a putative invader. "Nested" cryptic diversity, and the difficulties in correctly identifying invasive species that arise from it, represent a major challenge for managing biodiversity. [ABSTRACT FROM AUTHOR]

Abstract: Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases. [Copyright &y& Elsevier]

Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn; stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates. [ABSTRACT FROM AUTHOR]

Abstract: Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A ‘taxon duplication’ approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily. [Copyright &y& Elsevier]

Asteraceae are the largest family in southern Africa. Elucidating its origins and radiation in the region requires well-supported species-level phylogerms of the lineages. This paper presents a phylogenetic framework for subtribe Arctotidinae, which hose a southern and eastern African-Australian distribution centered in the winter-rainfall region of South Africa. DNA sequence data from five chloroplast fragments (ndhF, pshA-trnH, rps16, trnS-trnfM, and trnT-trnF) and the nuclear ITS region were analyzed separately and in combination using parsimony and Bayesian methods. The data sets comprised exemplars from 18 ingroup species, representing the five currently accepted genera, and four outgroup species thorn Gorteriinae. All analyses indicated Arctotis and Haplocarpha are polyphylelic as presently circumscribed. The Australian-endemic Cymbonotus lawsonianus was placed within a strongly supported elide also containing A. arctotoides from South Africa and H. schimperi from eastern Africa. Retention of Dymondia and resurrection of Landtia at generic level are strongly supported. The phylogenetic hypotheses indicate the subtribe might have originated in temperate southern or eastern Africa, or it was ancestrally widespread in southern Africa and has diversified vicariously. The derived placement of C. lawsonianus indicates long-distance dispersal from southern Africa to Australia occurred. [ABSTRACT FROM AUTHOR]