Kowiyou Yessoufou

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.

Large herbivores favour species diversity but have mixed impacts on phylogenetic community structure in an African savanna ecosystem

1;2;3 1;2;3 1;2;3 Summary 1. There has been much debate on the impact of large herbivores on biodiversity, especially given that large mammals are becoming locally extinct in many places. 2. The use of evolutionary information on community structure has typically been limited to evaluating assembly processes, for example, competition or habitat filtering, whereas a lack of long-term experiments has precluded the test of predictions considering more complex biotic interactions. 3. Reconstructing the complete phylogeny of the trees and shrubs of the Kruger National Park from DNA data, we tested for phylogenetic signal in antiherbivory traits and compared the phylogenetic structure of communities under various degrees of herbivore pressure using experimental plots spanning several decades. 4. We show that all antiherbivory traits examined demonstrated weak but significant phylogenetic signal, and that exclusion of large herbivores results in impoverished species diversity in restructured communities. Surprisingly, we also show that reduction in species diversity coupled with community reorganization does not necessarily result in a decrease in phylogenetic diversity, and that community responses to herbivore exclusion depend on initial structure. 5. Synthesis. Extinction of large mammal herbivores will have cascading effects on plant diversity; however, impacts on plant community structure are contingent on initial conditions. This research has implications for best practice when managing large herbivores and natural habitats.

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.

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.

Revisiting the impacts of non-random extinction on the tree-of-life

The tree-of-life represents the diversity of living organisms. Species extinction and the concomitant loss of branches from the tree-of-life is therefore a major conservation concern. There is increasing evidence indicating that extinction is phylogenetically non-random, such that if one species is vulnerable to extinction so too are its close relatives. However, the impact of non-random extinctions on the tree-of-life has been a matter of recent debate. Here, we combine simulations with empirical data on extinction risk in mammals. We demonstrate that phylogenetically clustered extinction leads to a disproportionate loss of branches from the tree-of-life, but that the loss of their summed lengths is indistinguishable from random extinction. We argue that under a speciational model of evolution, the number of branches lost might be of equal or greater consequences than the loss of summed branch lengths. We therefore suggest that the impact of non-random extinction on the tree-of-life may have been underestimated.

Revisiting Darwin's naturalization conundrum: explaining invasion success of non-native trees and shrubs in southern Africa

Summary 1. Invasive species are detrimental ecologically and economically. Their negative impacts in Africa are extensive and call for a renewed commitment to better understand the correlates of invasion success. 2. Here, we explored several putative drivers of species invasion among woody non-native trees and shrubs in southern Africa, a region of high floristic diversity. We tested for differences in functional traits between plant categories using a combination of phylogenetic independent contrasts and a simulation-based phylogenetic ANOVA. 3. We found that non-native species generally have longer flowering duration compared with native species and are generally hermaphroditic, and their dispersal is mostly abiotically mediated. We also revealed that non-native trees and shrubs that have become invasive are less closely related to native trees and shrubs than their non-invasive non-native counterparts. Non-natives that are more closely related to the native species pool may be more likely to possess traits suited to the new environment in which they find themselves and thus have greater chance of establishment. However, successful invaders are less closely related to the native pool, indicating evidence for competitive release or support for the vacant niche theory. 4. Synthesis. Non-native trees and shrubs in southern Africa are characterized by a suite of traits, including long flowering times, a hermaphroditic sexual system and abiotic dispersal, which may represent important adaptations promoting establishment. We suggest that differences in the evolutionary distances separating the native species pool from invasive and non-invasive species might help resolve Darwin’s naturalization conundrum.

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.

DNA Barcode Efficacy for the Identification of Economically Important Scale Insects (Hemiptera: Coccoidea) in South Africa

Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive groups of insects. They are sedentary, cryptic, and often resemble the plant parts that they feed on. This coupled with increased international trade in fresh agricultural produce, makes them a major quarantine risk. An important limitation in controlling these pests involves species identification. When scale insects are intercepted on imported produce, they must be rapidly and accurately identified, using morphology-based keys. This is time-consuming and requires extensive taxonomic experience. In addition, intercepted specimens are often immature or damaged, making identification difficult or impossible. A reliable complementary tool is needed for identification. DNA barcoding may be of great value for this purpose. In this study we investigate the suitability of the nuclear regions 18S and 28S as complementary DNA barcodes to the mitochondrial CO1 gene, across 10 scale insect families. Combining multiple criteria, our results indicate that the concatenation of CO1 and 28S greatly improves the identification success rate of scale insects to 91.5 %, demonstrating the utility of DNA barcoding in pest management.