Ingrid Parmentier

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees

Background DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species. Methodology/Principal Findings We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. Conclusions/Significance Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.

Are the living collections of the world's botanical gardens following species-richness patterns observed in natural ecosystems?

Pautasso M. and Parmentier I. 2007. Are the living collections of the world’s botanical gardens following species-richness patterns observed in natural ecosystems? Bot. Helv. 117: 15 – 28.Botanical gardens aim to promote the awareness, study and conservation of plant species diversity, but little is known about the species diversity of botanical gardens themselves. We therefore investigated whether the species richness of the world’s botanical gardens is related to their size, age and geographical location by compiling data from gardens in 124 different countries. The data show that even in these highly managed ecosystems, species richness can be described in terms of a relatively small number of large-scale patterns. As with most natural ecosystems, there were positive species-area and species-age relationships. There was also a positive latitudinal gradient in species richness, which contrasts with the trend observed in natural ecosystems. This discrepancy may be due to the use of heated greenhouses at high latitudes, the rarity of old botanical gardens in the tropics, and the problem of poverty in developing countries, where most hotspots of plant biodiversity are located. There is thus a need to allocate more funds to botanical gardens in species-rich regions. This study also calls for an increase in the coordination of data management between botanical gardens.

Prevalence of phylogenetic clustering at multiple scales in an African rain forest tree community

Summary 1. In highly diverse ecosystems, such as tropical forests, the relative importance of mechanisms underlying species coexistence (e.g. habitat filtering, competitive exclusion, neutral dynamics) is still poorly known and probably varies depending on spatial and phylogenetic scales. 2. Here, we develop new approaches for dissecting simultaneously the phylogenetic structure of communities at different phylogenetic depths and spatial scales. We tested with simulations that our method is able to disentangle overdispersion and clustering effects occurring at contrasted phylogenetic depths. 3. We applied our approaches to a 50 ha Forest Dynamic Plot located in Korup National Park (Cameroon) where 329,000 tree stems ≥ 1 cm in diameter were identified and mapped, and using a newly generated dated molecular phylogenetic tree based on 2 plastid loci (rbcL and matK), including 272 species from Korup (97% of the individuals). 4. Significant patterns of phylogenetic turnover were detected across 20 9 20 m 2 quadrats at most spatial scales, with higher turnover between topographic habitats than within habitats, indicating the prevalence of habitat filtering processes. Spatial phylogenetic clustering was detected over the entire range of phylogenetic depths indicating that competitive exclusion does not generate a pattern of phylogenetic overdispersion at this scale, even at a shallow phylogenetic depth. 5. Using an individual-based approach, we also show that closely related species tended to aggregate spatially until a scale of 1 m. However, the signal vanishes at smaller distance, suggesting that competitive exclusion can balance the impact of environmental filtering at a very fine spatial scale. 6. Synthesis. Using new methods to characterize the structure of communities across spatial and phylogenetic scales, we inferred the relative importance of the mechanisms underlying species coexistence in tropical forests. Our analysis confirms that environmental filtering processes are key in the structuring of natural communities at most spatial scales. Although negative-density tends to limit coexistence of closely related species at very short distance (<1 m), its influence is largely veiled by environmental filtering at larger distances.

La végétation des inselbergs de Piedra Nzas (Guinée Équatoriale continentale)

Abstract We report results from a phytosociological investigation of the vegetation of three inselbergs from continental Equatorial Guinea. Ten vegetation units belonging to five plant formations are described: grass-land, herbaceous fringe, shrubby fringe, forest fringe and saxicolous forest. One of the most striking plant communities on inselbergs are species-poor grassland on shallow soil, which comprise several species restricted to inselbergs. Forest fringes and the saxicolous forest have a high species diversity. Soil pH is strikingly low (pH 3,5–4,8). In the saxicolous forest, at 745 m altitude, a Podocarpus latifolius was found. This species usually lives at higher elevations (≥ 1500 m).

Morphological variability of the tallow tree, Pentadesma butyracea Sabine (Clusiaceae), in Benin

The seeds of Pentadesma butyracea (butter tree) are exploited by rural populations in West Africa to produce butter used for consumption and as an ingredient in cosmetics and medicinal preparations. To improve our knowledge of this under-studied species, the morphological variation of the trees, fruits and seeds in 12 natural populations of Benin distributed over a gradient of climate aridity is described with 14 quantitative and 13 qualitative descriptors. Most traits, except seed shape categories, show significant differences among populations. Multivariate analyses distinguish two eco-geographical groups: trees located in the more humid southern part of the species distribution are taller and have larger fruits and seeds than trees located in the north. To disentangle the relative roles of genetic variation and phenotypic plasticity in shaping, further phenotypic studies should be performed in common garden experiments.

Synopsis of the Genus Chamaeangis (Orchidaceae), Including Two New Taxa

Abstract A synopsis of Chamaeangis (Orchidaceae) with a taxonomic key to the genus is provided. Twelve taxa are recognized. Detailed examination of the specimens revealed two novelties: Chamaeangis spiralis from Nigeria and Cameroon, and Chamaeangis lecomtei var. tenuicalcar, a new variety from Ivory Coast, Ghana, and Gabon. Chamaeangis auciflora is shown to be synonymous with Chamaeangis letouzeyi, which is here redescribed in detail. Chamaeangis thomensis is neotypified, and Chamaeangis lecomtei var. lecomtei is lectotypified. Chamaeangis gracilis is treated as an excluded species. Several new country records of Chamaeangis are provided.

Species-richness of the living collections of the world’s botanical gardens — patterns within continents

SummaryThe broad aims of most botanic gardens are to promote the knowledge, conservation and use of plant biodiversity. The living collections of all but the most recently founded botanical gardens are the outcome of the work of generations of botanists. However, there has been little historical co-ordination between different gardens in assembling these collections. It is thus fascinating that these mostly artificial ecosystems follow two of the major biogeographical patterns observed in nature (a significant positive species-area and species-age relationship) when pooling data from all over the world. An open question is whether such patterns are confirmed when analysing the available data for the various landmasses. We found that the positive species-area and species-age relationships of the living collections of botanic gardens are confirmed when analysing data for (1) the Americas, (2) Africa and Europe, and (3) Asia and Australia. When controlling for spatial autocorrelation these groups of botanic gardens differ from the worldwide analysis in showing no significant positive latitudinal gradient in species richness. This result is still a discrepancy from the negative latitudinal gradient commonly observed in nature and confirms the necessity to better sustain botanic gardens in the tropics. Also when subdividing the analysis within continents, it is possible to describe a substantial amount of variation in the living collections of the world’s botanic gardens with a relatively small number of broad-scale patterns. This study supports the view that there is a need for an increased co-ordination in the conservation activities of the various botanical gardens.