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

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.     

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.     

Revisiting species delimitation within the genus Oxystele using DNA barcoding approach

The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus.     

Is high species richness at intermediate disturbance level valuable for phylogenetic conservation? A test on bird species in South‐East Botswana

The intermediate disturbance hypothesis (IDH) is one of the most debated theories in ecology. However, even when evidence is provided to support the hypothesis, its relevance for phylogenetic conservation has rarely been tested. Here, we investigated this question on birds in the South‐East district of Botswana along a disturbance gradient across three types of landscapes. We first reconstructed the phylogeny for all species recorded. Next, we assessed the relationship between dissimilarity measures and habitat types using the permutational MANOVA. Finally, we tested the IDH by fitting a generalized linear mixed effect model to account for errors due to spatial pseudo‐replications of our collection design. We found that, although species richness and phylogenetic diversity (PD) follow the prediction of the IDH, the evolutionary component of PD (i.e. PSV, phylogenetic species variability) contributes little to the prediction, suggesting that the correlation between PD and disturbance level is driven by the richness component of PD (i.e. PSR, phylogenetic species richness). However, the increased richness at the intermediate disturbance level does not result in phylogenetically diverse bird communities, indicating that the IDH contributes little to phylogenetic diversity. Our study adds to the body of literature questioning the relevance of IDH in ecology.     

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.     

Differences in evolutionary history translate into differences in invasion success of alien mammals in South Africa

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 study indicates that latitude, gestation length, social group size, and human population density are only marginal determinant of the variation in invasion success. However, we found that evolutionary distinctiveness – a parameter characterising the uniqueness of each alien species – is the most important predictive variable. Our results indicate that the invasive behavior of alien mammals may have been “fingerprinted” in their evolutionary past, and that evolutionary history might capture beyond ecological, biological and life‐history traits usually prioritized in predictive modeling of invasion success. These findings have applicability to the management of alien mammals in South Africa.     

Integrating biogeography,threat and evolutionary data to explore extinction crisis in the taxonomic group of cycads

Will the ongoing extinction crisis cause a severe loss of evolutionary information accumulated over millions of years on the tree of life? This question has been largely explored, particularly for vertebrates and angiosperms. However, no equivalent effort has been devoted to gymnosperms. Here, we address this question focusing on cycads, the gymnosperm group exhibiting the highest proportion of threatened species in the plant kingdom. We assembled the first complete phylogeny of cycads and assessed how species loss under three scenarios would impact the cycad tree of life. These scenarios are as follows: (1) All top 50% of evolutionarily distinct (ED ) species are lost; (2) all threatened species are lost; and (3) only all threatened species in each IUCN category are lost. Finally, we analyzed the biogeographical pattern of cycad diversity hotspots and tested for gaps in the current global conservation network. First, we showed that threatened species are not significantly clustered on the cycad tree of life. Second, we showed that the loss of all vulnerable or endangered species does not depart significantly from random loss. In contrast, the loss of all top 50% ED , all threatened or all critically endangered species, would result in a greater loss of PD (Phylogenetic Diversity) than expected. To inform conservation decisions, we defined five hotpots of diversity, and depending on the diversity metric used, these hotspots are located in Southern Africa, Australia, Indo‐Pacific, and Mexico and all are found within protected areas. We conclude that the phylogenetic diversity accumulated over millions of years in the cycad tree of life would not survive the current extinction crisis. As such, prioritizing efforts based on ED and concentrating efforts on critically endangered species particularly in southern Africa, Australia, Indo‐Pacific, and Mexico are required to safeguarding the evolutionary diversity in the cycad tree of life.     

Docosahexaenoic acid reduces suppressive and migratory functions of CD4CD25 regulatory T-cells

Immunological tolerance is one of the fundamental aspects of the immune system. The CD4⁺CD25⁺ regulatory T (Treg) cells have emerged as key players in the development of tolerance to self and foreign antigens. However, little is known about the endogenous factors and mechanisms controlling their suppressive capacity on immune response. In this study, we observed that docosahexaenoic acid (DHA), an n-3 polyunsaturated fatty acid, diminished, in a dose-dependent manner, the capacity of Treg cells to inhibit the CD4⁺CD25⁻ effector T-cell proliferation. DHA not only reduced the migration of Treg cells toward chemokines but also downregulated the mRNA expression of CCR-4 and CXCR-4 in Treg cells. DHA also curtailed ERK1/2 and Akt phosphorylation and downregulated the Smad7 levels in these cells. Contradictorily, DHA upregulated the mRNA expression of Foxp3, CTLA-4, TGF-β, and IL-10; nonetheless, this fatty acid increased the expression of p27^KIP1 mRNA, known to be involved in Treg cell unresponsiveness. In Foxp3-immunoprepitated nuclear proteins, DHA upregulated histone desacetylase 7 levels that would again participate in the unresposnsiveness of these cells. Finally, a DHA-enriched diet also diminished, ex vivo, the suppressive capacity of Treg cells. Altogether, these results suggest that DHA, by diminishing Treg cell functions, may play a key role in health and disease.     

A phylogenetic approach towards understanding the drivers of plant invasiveness on Robben Island,South Africa

Invasive plant species are a considerable threat to ecosystems globally and on islands in particular where species diversity can be relatively low. In this study, we examined the phylogenetic basis of invasion success on Robben Island in South Africa. The flora of the island was sampled extensively and the phylogeny of the local community was reconstructed using the two core DNA barcode regions, rbcLa and matK. By analysing the phylogenetic patterns of native and invasive floras at two different scales, we found that invasive alien species are more distantly related to native species, a confirmation of Darwin's naturalization hypothesis. However, this pattern also holds even for randomly generated communities, therefore discounting the explanatory power of Darwin's naturalization hypothesis as the unique driver of invasion success on the island. These findings suggest that the drivers of invasion success on the island may be linked to species traits rather than their evolutionary history alone, or to the combination thereof. This result also has implications for the invasion management programmes currently being implemented to rehabilitate the native diversity on Robben Island. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 142–152.