Papers by Michelle van der Bank
of constant diversification punctuated by a mass
Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination wi... more Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae. In:
ABSTRACTThere is growing evidence for a link between biodiversity and ecosystem function, and for... more ABSTRACTThere is growing evidence for a link between biodiversity and ecosystem function, and for a correlation between human population and the species diversity of plants and animals in a region. Here, we suggest these relationships might not be independent. Using a comprehensive phylogeny of southern African trees and structural equation modelling, we show that human population density correlates with tree phylogenetic diversity and show that this relationship is stronger than the correlation with species richness alone. Further, we demonstrate that areas high in phylogenetic diversity support a greater diversity of ecosystem goods and services, indicating that the evolutionary processes responsible for generating variation among living organisms are also key to the provisioning of nature’s contributions to people. Our results raise the intriguing possibility that the history of human settlement in southern Africa may have been shaped, in part, by the evolutionary history of its ...
Nature Precedings, 2008
A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the t... more A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene cox1, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as atpF-atpH and psbK-psbI, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed matK as the best candidate and suggested that in combination with trnH-psbA a slight increase in performance could be achieved. However, no study has tested the suitability of the newly proposed psbK-psbI and atpF-atpH for plant barcoding purposes. Four potential DNA barcodes, matK, trnH-psbA, atpF-atpH, and ps...
TAXON, 2012
Asphodelaceae subfam. Alooideae (Asparagales) currently comprises five genera, four of which are ... more Asphodelaceae subfam. Alooideae (Asparagales) currently comprises five genera, four of which are endemic to southern Africa. Despite their importance in commercial horticulture the evolutionary relationships among the genera are still incompletely understood. This study examines phylogenetic relationships in the subfamily using an expanded molecular sequence dataset from three plastid regions (matK, rbcLa, trnH-psbA) and the first subunit of the nuclear ribosomal internal transcribed spacer (ITS1). Sequence data were analysed using maximum parsimony and Bayesian statistics, and selected morphological traits were mapped onto the molecular phylogeny. Haworthia is confirmed as being polyphyletic, comprising three main clades that largely correlate with current subgeneric circumscriptions. Astroloba and Gasteria are evidently each monophyletic and sister respectively to Astroloba and H. subg. Robustipedunculares. Chortolirion is shown to be deeply nested within Aloe and is formally included in that genus. Aloe itself is clearly polyphyletic, with the dwarf species A. aristata allied to Haworthia subg. Robustipedunculares. The taxonomic implications of these findings are examined but branch support at critical lower nodes is insufficient at this stage to justify implementing major taxonomic changes.
Diversity and Distributions, 2017
Aim Floristic and faunal diversity fall within species assemblages that can be grouped into disti... more Aim Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present-day diversity patterns, and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present-day biogeographic assemblages, and highlight their conservation value. Location Southern Africa. Methods We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present-day structure emerges. We suggest present-day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region, and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat. Results We show the differentiation of most present-day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species-rich or threatened. Main conclusions Our approach complements analyses of the fossil record, and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.
Ecosphere, 2017
Invasive species are considered a major threat to ecosystem functioning and native biodiversity. ... more Invasive species are considered a major threat to ecosystem functioning and native biodiversity. Their negative impacts on ecosystems and the provisioning of ecosystem services have been widely documented. South Africa faces one of the most significant challenges from invasive species globally, and the South African government spent an estimated US $100 million to mitigate impacts of non-native species between 1995 and 2000 alone. Here, we modeled the current climatic niche of 162 non-native trees and shrubs within South Africa and explored potential shifts in their distribution with projected climate change. Our results indicate that over half of these species will experience a decrease in their suitable climate over the next decades, although not uniformly so and ranges are predicted to expand into some regions. We also compared recent vs. historical introductions and showed similar patterns, indicating that possible violation of equilibrium assumptions in our distribution models likely does not strongly influence our findings. We suggest that climate change may therefore provide a window of opportunity for more effective invasive species control within South Africa, but that large range shifts are likely for many nonnatives in the future, and new invasive threats might emerge.
BMC Evolutionary Biology, 2016
Background: Dioscorea is a widely distributed and highly diversified genus in tropical regions wh... more Background: Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or "elephant's foot" structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal. Results: The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet. Conclusions: Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin to just at the base or at the apex of it, or has been even replaced by an elaiosome.
Aliso, 2006
The phylogeny of Crocoideae, the largest of four subfamilies currently recognized in Tridaceae, h... more The phylogeny of Crocoideae, the largest of four subfamilies currently recognized in Tridaceae, has eluded resolution until sequences of two more plastid DNA regions were added here to a previously published matrix containing sequences from four DNA plastid regions. Sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia, Crocoideae are a climax group in lridaceae, comprising some 995 species, slightly more than half of the total in the family. Synapomorphies of Crocoideae include pollen exine perforate, pollen aperture operculate, ovule campylotropous (or hypotropous), root xylem vessels with simple perforations, cormous rootstock, inflorescence a spike, and plants deciduous. The six DNA region analysis here that includes examples of 27 of the 28 genera of the subfamily shows the southern African Tritoniopsis sister to the remaining genera, which resolve into four well-supported clusters (bootstrap support >85%). Each of these major clades is treated as a tribe, the synapomorphies of which are discussed in light of the molecular phylogenetic analyses. Original embryological and seed developmental studies largely support the tribal classification. Tritoniopsideae alone has the inner floral bracts not forked apically, and a hypotropous ovule, while this tribe and Watsonieae have axillary corm development. The remaining three tribes have apical corm development, and together with Watsonieae have a campylotropous ovule, and the inner layer of the inner integument crushed at maturity.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Jan 5, 2016
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent ... more Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using e...
Genome, 2017
Although a standard DNA barcode has been identified for plants, it does not always provide specie... more Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers an...
Proceedings of the National Academy of Sciences of the United States of America, Sep 6, 2016
Savannas first began to spread across Africa during the Miocene. A major hypothesis for explainin... more Savannas first began to spread across Africa during the Miocene. A major hypothesis for explaining this vegetation change is the increase in C4 grasses, promoting fire. We investigated whether mammals could also have contributed to savanna expansion by using spinescence as a marker of mammal herbivory. Looking at the present distribution of 1,852 tree species, we established that spinescence is mainly associated with two functional types of mammals: large browsers and medium-sized mixed feeders. Using a dated phylogeny for the same tree species, we found that spinescence evolved at least 55 times. The diversification of spiny plants occurred long after the evolution of Afrotherian proboscideans and hyracoids. However, it is remarkably congruent with diversification of bovids, the lineage including the antelope that predominantly browse these plants today. Our findings suggest that herbivore-adapted savannas evolved several million years before fire-maintained savannas and probably, ...
South African Journal of Botany, 2008
The Ophiostomatoid fungi include five genera, including Ceratocystis and Ophiostoma, two genera w... more The Ophiostomatoid fungi include five genera, including Ceratocystis and Ophiostoma, two genera which include several important tree pathogens. They are mostly vectored by insects, that either wound trees or visit wounds due to other causes, thus spreading the fungi between trees. Ceratocystis and Ophiostoma include important canker and wilt pathogens such as C. albifundus that causes wilt and dieback of Acacia mearnsii trees in South Africa, C. fagacearum the cause of oak wilt in the USA, and the Dutch elm disease pathogens O. ulmi and O. novo-ulmi. Many other species cause sapstain of lumber, reducing its commercial value. Very little is known regarding species of Ceratocystis and Ophiostoma from South Africa, especially on native trees. Surveys were thus conducted to collect Ceratocystis and Ophiostoma species infecting wounds on native trees in South Africa. Both morphological studies and multigene phylogenies were used to identify the fungi collected. The pathogenicity of selected species was also considered using artificial inoculations under glasshouse conditions. Numerous Ceratocystis and Ophiostoma species and their anamorph states were collected from native tree species spanning eight different genera and six families, growing in three geographical regions of South Africa. Pesotum quercus, P. fragrans and C. albifundus, as well as a new Ophiostoma sp. were collected. Two undescribed species of Ceratocystis were also discovered. Inoculation studies using the two new Ceratocystis resulted in lesions on Rapanea melanophloeos, Sclerocarya birrea and Acacia nigrescens. The diversity of the fungi collected, from a relatively limited survey, and the fact that potentially unknown tree pathogens have emerged, provides concrete evidence that the diversity and biology of Ceratocystis and Ophiostoma on native trees is poorly understood and deserves further study in South Africa.
The New phytologist, 2016
Finckh et al. (2016; this issue of New Phytologist, pp. 904–909) query our inferences drawn from ... more Finckh et al. (2016; this issue of New Phytologist, pp. 904–909) query our inferences drawn from a recent study (Maurin et al., 2014) on the evolutionary origins of the geoxylic suffrutex life form in southern Africa. Geoxylic suffrutices, or more informally ‘underground trees’ represent a distinct growth form characterized by a long-lived woody xylopodia underground with often short lived aerial shoots (White, 1979; Simon & Pennington, 2012). Described in detail by White (1979), ‘geoxyles’ are common in fire-dependent savanna ecosystems. Using a time calibrated phylogenetic tree for the woody taxa of southern Africa, sampling 1400 taxa, we showed that the geoxylic suffrutex life form evolved independently multiple times, suggesting a selective advantage to going ‘underground’ (Maurin et al., 2014). We reviewed four putative drivers of the geoxyle habit: (1) winter frost on the South African Highveld, proposed by Burtt Davy (1922); (2) mammal herbivory; (3) edaphic factors, particularly seasonal waterlogging; and (4) fire. We discussed evidence in support of each, and found that escape from fire is the most general explanation. We noted that ‘poor growing conditions that reduce growth rates of juvenile trees would also result in reduced probabilities of reaching fire-proof sizes and transitioning to tall mature trees’ and that ‘geoxyles are common where site conditions reduce growth rates, such as on seasonally waterlogged and/or low-nutrient soils, or, . . . at high-altitude sites with cold winters’ (Maurin et al., 2014). Finckh et al. (2016) suggest we may have overestimated the link with fire, and overlooked the importance of frost; we revisit their arguments.
Annual Research & Review in Biology, 2015
Aim: The aim of this study was to estimate divergence ages and reconstruct ancestral areas for th... more Aim: The aim of this study was to estimate divergence ages and reconstruct ancestral areas for the clades within Combretaceae. Methods: We utilized a comprehensive dataset of 144 species of Combretaceae with a worldwide sampling to reconstruct a dated phylogeny based on a Bayesian analysis of five gene regions (ITS, rbcL, matK, psaA-yf3 and trnH-psbA). Bayesian phylogenetic tree was generated using a Bayesian MCMC approach implemented in BEAST v.1.7.5 to generate lineage dating. Two fossils Dilcherocarpon Combretoides (93.5-112 mya) and Terminalioxylon (28 mya) were used for Original Research Article Gere et al.; ARRB, 8(5): 1-20, 2015; Article no.ARRB.17476 2 calibration. S-DIVA and DEC model analysis were used to estimate ancestral area ranges. Results: Our results indicate that the earliest diversification of Combretaceae occured ca. 110 mya. This was followed by the splitting of the family into two subfamilies, Combretoideae and Strephonematoideae during the Late Cretaceous period. This event followed the radiation of Combretoideae, ca 105.6 mya to give rise to two tribes, Combretaeae and Laguncularieae which diverged around 60.9 mya and 52.9 mya, respectively. The two main subtribes Combretineae and Terminaliinae, radiated at ca. 48.3 and 46.4 mya respectively. African continent is inferred as the origin of Combretaceae, with dispersal as the major event responsible for the intercontinental disjunct distribution observed in the tropical and subtropical regions. Main Conclusions: Our results revealed that the crown age of Combretaceae is ca.110 mya, a time hypothesised to be marked by high angiosperm diversification. Two largest subtribes Combretineae and Terminaliinae, split occurred in the Late Cretaceous period with divergence estimated at the commencement of Eocene epoch. The African continent is hypothesised to have emerged from the split of the super continent Gondwana. Long distance dispersal is postulated as the major modeller, with vicariance and extinction playing marginal roles in shaping the current intercontinental disjunct distribution of Combretaceae in the tropical and subtropical regions of the world.
AoB PLANTS, Jan 27, 2015
Large-scale DNA barcoding provides a new technique for species identification and evaluation of r... more Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK+rbcLa) dataset as a better barcode than single regions. We found a high score (100%) of correct identification of individuals to their respective genera but very low score (<50%) in identifying them to species. We found a considerable match (54%) between genetic species and...
South African Journal of Botany
Africa's cycads are highly threatened with four species reported to be extinct in the wild. A... more Africa's cycads are highly threatened with four species reported to be extinct in the wild. Although trade and utilization of cycads are strictly legislated both in South Africa and internationally, cycads are still under threat especially from illegal collectors for horticultural and medicinal purposes. Efforts to control these threats are confounded by the fact that illegal samples are often devoid of diagnostic features making it difficult to provide a reliable identification needed for prosecution. The objective of this study was to assist morphology-based identification using DNA barcoding approach. We focused on Encephalartos Lehm. (Zamiaceae), a genus entirely endemic to Africa with 65 currently defined morpho-species. Conducting a thorough taxon sampling, and testing the discriminatory power of single and combined DNA regions, we showed that the combination of rbcLa + matK + nrITS provides the highest barcode potential, albeit with a non-satisfactory discriminatory power...
Ecology and Evolution
Attempts to investigate the drivers of invasion success are generally limited to the biological a... more Attempts to investigate the drivers of invasion success are generally limited to the biological and evolutionary traits distinguishing native from introduced species. Although alien species introduced to the same recipient environment differ in their invasion intensity – for example, some are “strong invaders”; others are “weak invaders” – the factors underlying the variation in invasion success within alien communities are little explored. In this study, we ask what drives the variation in invasion success of alien mammals in South Africa. First, we tested for taxonomic and phylogenetic signal in invasion intensity. Second, we reconstructed predictive models of the variation in invasion intensity among alien mammals using the generalized linear mixed-effects models. We found that the family Bovidae and the order Artiodactyla contained more “strong invaders” than expected by chance, and that such taxonomic signal did not translate into phylogenetic selectivity. In addition, our stud...
ABSTRACT Medicinal plants cover a broad range of taxa which may be phylogenetically less related ... more ABSTRACT Medicinal plants cover a broad range of taxa which may be phylogenetically less related but morphologically very similar. Such similarity between species of different medicinal uses may also lead to misidentification and inappropriate use. The identification may even be more problematic as medicinal plants are traded as dried or processed leaves, roots, barks, or extracts completely devoid of morphological features. Misidentification of medicinal plants and subsequent misuses are of high concern given that several medicinal plants are poisonous. In the current study we targeted the most commonly used medicinal plants in South Africa and produced a set of barcodes for fast and easy DNA-based species identification. We tested the efficacy of core barcodes in identification of medicinal plants and their ability to assign poorly conserved plant organs to corresponding species. In general DNA barcodes provide very high discriminatory power, indicating the effectiveness of barcoding approach in verifying the identity of at least the most common plant organs traded in South African medicinal markets.
Diversity and Distributions, 2014
Aim Biodiversity hotspots have important roles in conservation prioritisation, but efficient meth... more Aim Biodiversity hotspots have important roles in conservation prioritisation, but efficient methods for selecting among them remain debated. Location Southern Africa. Methods In this study, we used data on the dated phylogeny and geographical distribution of 1400 tree species in southern Africa to map regional hotspots of species richness (SR), phylogenetic diversity (PD), phylogenetic endemism (PE), species endemism (CWE), and evolutionary distinctiveness and global endangerment (EDGE). In addition, we evaluated the efficiency of hotspots in capturing complementary areas of species richness and phylogenetic diversity. We examined the spatial overlap among hotspots for each metric, and review how well one metric may serve as a surrogate for others. We then evaluated the effectiveness of current conservation areas in capturing these different facets of diversity and complementary areas. Lastly, we explored the environmental factors influencing the distribution of these diversity metrics in southern Africa. Results We reveal large spatial incongruence between biodiversity indices, resulting in unequal representation of PD, SR, PE, CWE and EDGE in hotspots and currently protected areas. Notably, no hotspot area is shared among all five measures, and 69% of hotspot areas were unique to a single diversity metric. Areas selected using complementarity are even more dispersed, but capture rare diversity that is overlooked by the hotspot approach. Main conclusions An integrative approach that considers multiple facets of biodiversity is needed if we are to maximise the conservation of tree diversity in southern Africa.
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Papers by Michelle van der Bank