Barnabas H. Daru

A Global Trend towards the Loss of Evolutionarily Unique Species in Mangrove Ecosystems

The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.

Spiny plants, mammal browsers, and the origin of African savannas

Significance Africa hosts contrasting communities of mammal browsers and is, thus, the ideal background for testing their effect on plant communities and evolution. In this study at the continental scale, we reveal which mammal browsers are most closely associated with spiny communities of trees. We then show a remarkable convergence between the evolutionary histories of these browsers (the bovids) and spiny plants. Over the last 16 My, plants from unrelated lineages developed spines 55 times. These convergent patterns of evolution suggest that the arrival and diversification of bovids in Africa changed the rules for persisting in woody communities. Contrary to our current understanding, our data suggest that browsers predate fire by millions of years as agents driving the origin of savannas. 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, in different environmental conditions. Spiny savannas with abundant mammal herbivores occur in drier climates and on nutrient-rich soils, whereas fire-maintained savannas occur in wetter climates on nutrient-poor soils.

Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae

Abstract Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK) for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA) to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.

Phylogenetic Patterns of Extinction Risk in the Eastern Arc Ecosystems, an African Biodiversity Hotspot

There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains – an important African biodiversity hotspot – and described the distribution of extinction risk across taxonomic ranks and phylogeny. We provide evidence for both taxonomic and phylogenetic selectivity in extinction risk. However, we found that selectivity varies with IUCN extinction risk category. Vulnerable species are more closely related than expected by chance, whereas endangered and critically endangered species are not significantly clustered on the phylogeny. We suggest that the general observation for taxonomic and phylogenetic selectivity (i.e. phylogenetic signal, the tendency of closely related species to share similar traits) in extinction risks is therefore largely driven by vulnerable species, and not necessarily the most highly threatened. We also used information on altitudinal distribution and climate to generate a predictive model of at-risk species richness, and found that greater threatened species richness is found at higher altitude, allowing for more informed conservation decision making. Our results indicate that evolutionary history can help predict plant susceptibility to extinction threats in the hyper-diverse but woefully-understudied Eastern Arc Mountains, and illustrate the contribution of phylogenetic approaches in conserving African floristic biodiversity where detailed ecological and evolutionary data are often lacking.

A Molecular Phylogeny and Generic Classification of Asphodelaceae subfamily Alooideae: A Final Resolution of the Prickly Issue of Polyphyly in the Alooids?

Abstract Phylogenetic analysis of plastid (rbcLa, matK, trnH-psbA and the trnL intron) and nuclear (ITS1) sequence datasets in a wide sampling of species of Asphodelaceae: Alooideae provides a generally well-resolved phylogeny. Among traditionally accepted genera only Astroloba and Gasteria are supported as monophyletic. Species of Haworthia are distributed among three clades corresponding to the current subgenera. Aloe s. l. (including Chortolirion) segregates into six, well-supported clades corresponding respectively to sections Dracoaloe (= Aloidendron), Kumara + Haemanthifoliae, Macrifoliae, Aristatae, Serrulatae, and the remainder of the genus. The first three clades are retrieved as early branching lineages, whereas A. sects. Aristatae and Serrulatae are strongly supported as members of a clade including Astroloba + Haworthia subg. Robustipedunculatae. We examine possible options for recircumscribing the genera of Alooideae as reciprocally monophyletic entities. Although morphological and molecular data are consistent with expansion of Aloe to include all members of Alooideae, we accept and implement an alternative option maintaining historical usage in the group as far as possible. Astroloba and Gasteria are retained as currently circumscribed; Haworthia is restricted to H. subg. Haworthia; the genus Tulista is accepted for members of H. subg. Robustipedunculatae, with the new combination T. minima; and H. subg. Hexangulares is treated as the genus Haworthiopsis with the new combinations H. koelmaniorum, H. pungens, and H. tessellata. The genus Aloe is restricted to the clade comprising the ‘true aloes’, with Aloidendron, Aloiampelos, and Kumara accepted as segregates, the latter broadened to include A. haemanthifolia as K. haemanthifolia. Aloe aristata is segregated in the monotypic genus Aristaloe as A. aristata and Aloe sect. Serrulatae is treated as the new genus Gonialoe with the species G. dinteri, G. sladeniana, and G. variegata.

Phylogenetic exploration of commonly used medicinal plants in South Africa

The rapid growth rate of human population, along with the public health crisis encountered in many regions, particularly in developing world, creates an urgent need for the discovery of alternative drugs. Because medicinal plants are not distributed randomly across lineages, it has been suggested that phylogeny along with traditional knowledge of plant uses can guide the identification of new medicinally useful plants. In this study, we combined different statistical approaches to test for phylogenetic signal in 33 categories of plant uses in South Africa. Depending on the null models considered, we found evidence for signal in up to 45% of plant use categories, indicating the need for multiple tests combination to maximize the chance of discovering new medicinal plants when applying a phylogenetic comparative approach. Furthermore, although there was no signal in the diversity of medicinal uses—that is, total number of medicinal uses recorded for each plant—our results indicate that taxa that are evolutionarily closely related have significantly more uses than those that are evolutionarily isolated. Our study therefore provides additional support to the body of the literature that advocates for the inclusion of phylogeny in bioscreening medicinal flora for the discovery of alternative medicines.

Evidence of constant diversification punctuated by a mass extinction in the African cycads.

The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.

DNA BARCODING REVEALS MICRO-EVOLUTIONARY CHANGES AND RIVER SYSTEM-LEVEL PHYLOGEOGRAPHIC RESOLUTION OF AFRICAN SILVER CATFISH, SCHILBE INTERMEDIUS (ACTINOPTERYGII: SILURIFORMES: SCHILBEIDAE) FROM SEVEN POPULATIONS ACROSS DIFFERENT AFRICAN RIVER SYSTEMS

Background. Under the tropics, less than 40% of known fishes are identified to species-level. Further, the ongo- ing global change poses unprecedented threat to biodiversity, and several taxa are likely to go extinct even before they could be described. Traditional ecological theory suggests that species would escape extinction risk posed by global threats (e.g., climate change) only by migrating to new environments. In this study, we hypothesise that micro-evolutionary changes (evolution within species and populations) are also important mechanisms for the survival of Schilbe intermedius in Africa, a continent subjected to uneven distribution of climate severity. Materials and methods. Using the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as animal DNA barcode, we tested this hypothesis by analysing the genetic diversity and phylogenetic relations between seven populations of S. intermedius across different African river systems. Results. We reveal a clear geographical patterning in genetic variations, with three clear clusters (southern Africa, eastern Africa, and western Africa). In southern Africa, the South African population is distinct from that of Namibia and Botswana. In addition, within Nigerian populations of silver catfish, two sub-clusters emerged from two isolated river systems. We suggest that the phylogeographic pattern within African silver catfish pop- ulations mirror the past effects of selection and gene flow, and that the split within Nigerian silver catfish popu- lations might be the result of micro-evolutionary adaptive responses to local selection pressures. Conclusion. We suggest that the strong genetic difference in African silver catfish among geographically isolat- ed river systems might be the result of in situ micro-evolutionary adaptive responses to changing environments, and that DNA barcode has potential beyond species delimitation.

Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine

Abstract Medicinal plants cover a broad range of taxa, which may be phylogenetically less related but morphologically very similar. Such morphological similarity between species may lead to misidentification and inappropriate use. Also the substitution of a medicinal plant by a cheaper alternative (e.g. other non-medicinal plant species), either due to misidentification, or deliberately to cheat consumers, is an issue of growing concern. In this study, we used DNA barcoding to identify commonly used medicinal plants in South Africa. Using the core plant barcodes, matK and rbcLa, obtained from processed and poorly conserved materials sold at the muthi traditional medicine market, we tested efficacy of the barcodes in species discrimination. Based on genetic divergence, PCR amplification efficiency and BLAST algorithm, we revealed varied discriminatory potentials for the DNA barcodes. In general, the barcodes exhibited high discriminatory power, indicating their effectiveness in verifying the identity of the most common plant species traded in South African medicinal markets. BLAST algorithm successfully matched 61% of the queries against a reference database, suggesting that most of the information supplied by sellers at traditional medicinal markets in South Africa is correct. Our findings reinforce the utility of DNA barcoding technique in limiting false identification that can harm public health.

Understanding the Processes Underpinning Patterns of Phylogenetic Regionalization

A key step in understanding the distribution of biodiversity is the grouping of regions based on their shared elements. Historically, regionalization schemes have been largely species centric. Recently, there has been interest in incorporating phylogenetic information into regionalization schemes. Phylogenetic regionalization can provide novel insights into the mechanisms that generate, distribute, and maintain biodiversity. We argue that four processes (dispersal limitation, extinction, speciation, and niche conservatism) underlie the formation of species assemblages into phylogenetically distinct biogeographic units. We outline how it can be possible to distinguish among these processes, and identify centers of evolutionary radiation, museums of diversity, and extinction hotspots. We suggest that phylogenetic regionalization provides a rigorous and objective classification of regional diversity and enhances our knowledge of biodiversity patterns.