Piet Stoffelen

Exploring the floristic diversity of tropical Africa

BackgroundUnderstanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO – one of the largest mega-databases of tropical African vascular plant species distributions ever compiled – to address questions about plant and growth form diversity across tropical Africa.ResultsThe filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5–7% of the estimated world’s tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic.ConclusionsThe botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa’s unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011–2020.

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

RAINBIO: a mega-database of tropical African vascular plants distributions

Abstract The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

A new species of Coffea (Rubiaceae) and notes on Mount Kupe (Cameroon)

Summary. A new Cameroonian species, Coffea montekupensis (Rubiaceae, Coffeeae) is described and morphological and ecological documentation supplied. C. montekupensis is endemic to the Bakossi Mountains and all but one of the known collections are from Mount Kupe. It resembles the more widely distributed C. brevipes Hiern which also occurs on Mount Kupe, although the two are not sympatric.

Pollen morphology of Coffea and Psilanthus (Rubiaceae-Coffeeae), mainly from Africa

Twenty‐six Coffea and six Psilanthus species are examined to provide a survey of the pollen morphological variation of the African Coffeeae. These observations are compared with data from literature and evaluated by numerical analysis. The latter corroborates that the two genera are distinguishable on the basis of pollen morphology. Coffea grains are generally 3‐colporate, while Psilanthus mostly has 4–5‐colporate grains. In Coffea many species show a surprisingly high degree of pollen polymorphism. There is no doubt that this phenomenon is at least in part responsible for the poor taxonomic value of pollen features at the specific level, in this genus. As regards Psilanthus our results seem to indicate pollen morphological differences between African (more narrow muri; no supratectal ornamentation) and Asian species (muri wider; supratectal granules), but this should be confirmed by investigating more species. This is in contradiction to the actual division in subg. Psilanthus and subg. Afrocoffea.

Metabolomics fingerprint of coffee species determined by untargeted-profiling study using LC-HRMS

Coffee bean extracts are consumed all over the world as beverage and there is a growing interest in coffee leaf extracts as food supplements. The wild diversity in Coffea (Rubiaceae) genus is large and could offer new opportunities and challenges. In the present work, a metabolomics approach was implemented to examine leaf chemical composition of 9 Coffea species grown in the same environmental conditions. Leaves were analyzed by LC-HRMS and a comprehensive statistical workflow was designed. It served for univariate hypothesis testing and multivariate modeling by PCA and partial PLS-DA on the Workflow4Metabolomics infrastructure. The first two axes of PCA and PLS-DA describes more than 40% of variances with good values of explained variances. This strategy permitted to investigate the metabolomics data and their relation with botanic and genetic informations. Finally, the identification of several key metabolites for the discrimination between species was further characterized.

Reproductive isolation, gene flow and speciation in the former Coffea subgenus: a review

Key messageThe formerCoffeasubgenus is a species complex showing qualitative gene flow and reproductive barriers between species. Such qualitative gene flow allowed its evolution over time, particularly during the successive forest expansion-regression cycles in relation with glaciation periods.AbstractThe present paper reviews the main botanical, geographical and genetic characteristics of the Coffea genus and then focuses on the former Coffea subgenus. Its broad distribution in Africa, Madagascar and Mascarene Islands is related to the high diversity of ecological situations. The importance of sympatry and parapatry cases and their role on gene flow possibilities between species is then underlined in the paper. Such gene flow is nevertheless partially limited by reproductive barriers: flowering date, frequency of hybrid F1 emergence, as well as the vigor and fertility of such hybrids. When hybridization occurs, distortion of segregation and disruptive selection would allow qualitative flow of non-adaptative genes, thus limiting the effect of genetic drift in small populations. The last part of the paper defines the notion of metaspecies in the case of the former Coffea by extension of the concept of metapopulation to species. The evolution over time of a metaspecies is finally discussed in relation with sympatry situations, gene flow possibilities and forest fragmentation.

Identification of coffee leaves using FT-NIR spectroscopy and SIMCA

Abundant literature has been devoted to coffee beans (green or roasted) chemical description but relatively few studies have been devoted to coffee leaves. Given the fact that coffee leaves are used for food and medicinal consumption, it was of interest to develop a rapid screening method in order to identify coffee leaves taxa. Investigation by Fourier - Transform near infrared spectroscopy (FT-NIRS) was performed on nine Coffea taxa leaves harvested over one year in a tropical greenhouse of the Botanic Garden Meise (Belgium). The only process after leaves harvesting was an effective drying and a homogeneous leaves grinding. FT-NIRS with SIMCA analysis allowed to discriminate the spectral profiles across taxon, aging stage (mature and senescence coffee leaves) and harvest period. This study showed that it was possible (i) to classify the different taxa, (ii) to identify their aging stage and (iii) to identify the harvest period for the mature stage with a correct classification rate of 99%, 100% and 90%, respectively.

Scientific user requirements for a herbarium data portal

Abstract The digitization of herbaria and their online access will greatly facilitate access to plant collections around the world. This will improve the efficiency of taxonomy and help reduce inequalities between scientists. The Botanic Garden Meise, Belgium, is currently digitizing 1.2 million specimens including label data. In this paper we describe the user requirements analysis conducted for a new herbarium web portal. The aim was to identify the required functionality, but also to assist in the prioritization of software development and data acquisition. The Garden conducted the analysis in cooperation with Clockwork, the digital engagement agency of Ordina. Using a series of interactive interviews, potential users were consulted from universities, research institutions, science-policy initiatives and the Botanic Garden Meise. Although digital herbarium data have many potential stakeholders, we focused on the needs of taxonomists, ecologists and historians, who are currently the primary users of the Meise herbarium data portal. The three categories of user have similar needs, all wanted as much specimen data as possible, and for those data, to be interlinked with other digital resources within and outside the Garden. Many users wanted an interactive system that they could comment on, or correct online, particularly if such corrections and annotations could be used to rank the reliability of data. Many requirements depend on the quality of the digitized data associated with each specimen. The essential data fields are the taxonomic name; geographic location; country; collection date; collector name and collection number. Also all researchers valued linkage between biodiversity literature and specimens. Nevertheless, to verify digitized data the researchers still want access to high quality images, even if fully transcribed label information is provided. The only major point of disagreement is the level of access users should have and what they should be allowed to do with the data and images. Not all of the user requirements are feasible given the current technical and regulatory landscape, however, the potential of these suggestions is discussed. Currently, there is no off-the-shelf solution to satisfy all these user requirements, but the intention of this paper is to guide other herbaria who are prioritising their investment in digitization and online web functionality.

Fibres in Meise Botanic Garden: A Future for Heritage Collections?

The precious historical collection of fibres in Meise Botanic Garden, with over 500 specimens in old hand-blown glass jars, was rehabilitated in 2017. Most of the specimens date back to the second half of the 19th century, a period of technological revolution. The rehabilitation retraces the industrious search for every possible raw material provided by nature at that time. The result is astonishing, not only regarding the origin and quality of the preserved material, its label information and its accompanying manuscripts, but also because of the extremely wide range of fibre species and their processing. Noted collectors enriching our collections were, inter alios, the Josephite Brother Bernardin of Melle (Belgium), Carl von Martius and his brother Theodor Martius of Erlangen (Germany) and Henri Van Heurck of Antwerp (Belgium). Famous museums and botanic gardens such as the Museum of French Colonies in Paris (France) and the Experimental Garden in Eala (Democratic Republic of the Congo DRC) were also important suppliers. Samples originate from all over the world with strong representation from India, the DRC and Brazil. The nature of the fibres in the collection is very diverse and ranges from stem, bark and leaf fibres to husk fibres and seed hairs. Some of them have been processed into bundles and braids, beaten bark, spun thread and twined rope, as well as rough or organza-like ‡ ‡ ‡ ‡