Fossil pollen as a record of past biodiversity

Quaternary pollen records may contribute uniquely to the understanding of present plant diversity. Pollen assemblages can reflect diversity at community and landscape scales but the time resolution of most studies does not match that of modern ecological studies. Because of the complicating effects of differential pollen productivity and dispersal, pollen records do not directly reflect equitability aspects of vegetation diversity. Vegetation diversity indices other than S (the total number of taxa) are therefore not appropriate for pollen assemblages. As a measure of the species richness palynological richness is biased by the lack of taxonomic precision, by a possible interference on pollen dispersal from vegetation structure and by pollen representation. The nonlinear relationship between species richness and pollen-taxa richness may be used in attempts to estimate past floristic richness from fossil pollen assemblages. Using a hypothetical example the strong effect of cover shifts in the vegetation affecting taxa with different representation (R_rel) values on observed palynological richness is demonstrated. It is suggested that estimates of relative pollen productivity should be used to guide the pollen sum on which pollen-type richness is estimated by rarefaction techniques and this approach is illustrated using a paired site study of late Holocene diversity dynamics. The need for a modern training set relating pollen-type richness to species richness, pollen productivity and vegetation structure is emphasized.     

DNA barcoding of South Africa’s ornamental freshwater fish – are the names reliable?

Trade in freshwater ornamental fish in South Africa is currently regulated by a ‘blacklist’ to prevent potentially invasive taxa from establishing in the country. Because its effective implementation requires accurate identification, the aim of the present study was to test whether DNA barcoding is a useful tool to identify freshwater fishes in the South African pet trade. A total of 351 aquarium fish specimens, representing 185 traded taxa, were sequenced for the mitochondrial COI barcoding marker in 2011 and 2012. Lake Malawi cichlids were treated as a single group due to a lack of resolution in their COI marker, resulting in a data set of 137 successfully sequenced taxa. The Barcode Of Life Database (BOLD) and GenBank were used for taxonomic assignment comparisons. The genetic identification matched the scientific name inferred from the trade name for 60 taxa (43.8%) using BOLD, and for 67 taxa (48.9%) using GenBank. A genetic ID could not be assigned in 47 (34.3%) cases using BOLD and in 37 cases (27%) using GenBank. Whereas DNA barcoding can be a useful tool to help identify imported freshwater fishes, it requires further development of publicly available databases to become a reliable means of identification.     

Notes on the key role of stenochoric endemic plants in the floristic regionalization of Yunnan

With the accumulation and accessibility of information about plant species, it is time to re-evaluate and further divide a global biodiversity hotspot region, Yunnan, located in southwestern China. In this study, we combined data on the distribution of 1010 stenochoric endemic seed plants, vegetation constitution, geological history and climate change, and used these to propose a new system of floristic regions. We identified 11 distinct floristic subregions and 84 floristic provinces within Yunnan. Our work confirmed some views emphasized by Wu Zhengyi that the stenochoric endemic species play a key role in defining floristic provinces; that stenochoric endemic plants with long collection and publication histories are more valuable; that greater attention should be paid to woody plants; and that for Yunnan, a border region, some trans-border distributed elements should be treated cautiously.     

Seed dispersal in a polder after partial tidal restoration: Implications for salt‐marsh restoration

Question: The vegetation in a polder after partial tidal restoration does not resemble the targeted salt‐marsh vegetation. Is this difference in vegetation due to lack of dispersal or unsuitable abiotic conditions? What could be done for a better restoration of the site? Location: Northwestern France. Methods: Seeds were trapped at the single inlet of the polder with a 200‐μ m mesh net to estimate inputs of seeds from the bay. In parallel, seed dispersal was studied in the polder by placing Astroturf® seed traps on the surface of the sediment at three different elevations in three distinct areas. Abiotic conditions such as flooding frequency, water table level and soil salinity were monitored. Results: All but one species from the adjacent salt marshes were trapped at the inlet. Not all of these species were on the seed traps inside the polder. Seed dispersal was not homogeneous in the polder and seed trap content mostly discriminated in function of their elevation. Salinity and water logging at the bottom of the slope were very high compared to tolerance of most halophytes but decreased rapidly higher up the slope. Conclusions: The development of salt marsh target species is highly restricted by limited hydrochory inside the polder but also by unfavourable soil conditions induced by the actual hydrological regime. Halophytes are excluded at the bottom of the slope by abiotic conditions and out‐competed by sub‐halophytes higher up. In order to restore salt marsh vegetation inside the polder, a larger opening should be induced in order to increase the flooded surface, and diminish water logging and flooding frequencies.     

Biobanking for Europe

Biobanks are well-organized resources comprising biological samples and associated information that are accessible to scientific investigation. Across Europe, millions of samples with related data are held in different types of collections. While individual collections can be well organized and accessible, the resources are subject to fragmentation, insecurity of funding and incompleteness. To address these issues, a Biobanking and BioMolecular Resources Infrastructure (BBMRI) is to be developed across Europe, thereby implementing a European 'roadmap' for research infrastructures that was developed by a forum of EU member states and that has been received by the European Commission. In this review, we describe the work involved in preparing for the construction of BBMRI in a European and global context.     

Plant diversity in managed sal (Shorea robusta Gaertn.) forests of Gorakhpur, India: species composition, regeneration and conservation

The sal (Shorea robusta) forest vegetation of Sohagibarawa Wildlife Sanctuary, Gorakhpur, India was analysed to assess plant diversity, regeneration pattern and the status of species conservation. A total of 208 plant species representing 165 genera and 72 families were recorded. Species richness, mean density and basal area of individuals in the observed forest were compared with those of other sal-dominated forests of India. The sal forest was rich in Papilionaceae (23 species), which contributed maximally to the total number of individuals of <30 cm girth. After sal, density was maximal for a leguminous shrub, Moghania chappar. In addition to the usual recruitment by seed, a number of species also showed non-seed regeneration through storage roots, sprouts or ramet proliferation. The individuals regenerating as sprouts from underground stem or storage organs contributed significantly to the sum total of individuals/ha. As much as 45.5% of the total individuals were of ramet origin and shared 10.6% of the total species richness of the forest. In stands facing moderate to low disturbance, thickets of dense entangled mass of vegetation, predominantly composed of thorny lianas, were identified that usually contained less common and rare species like Rauwolfia serpentina, Desmodium latifolium, Crotalaria alata and Gloriosa superba in addition to the frequent ones. These thickets help to conserve the special habitat conditions and provide protection for natural regeneration of several infrequent and rare plant species and thus contribute towards the maintenance and in situ conservation of overall diversity of recurrently disturbed forest vegetation.     

The Atlantic elements in the Swiss flora: distribution, diversity, and conservation status

The purpose of this study was to examine the composition, distribution, ecology, and conservation status of the Atlantic elements of the Swiss flora. About 195 Atlantic and 80 Mediterranean–Atlantic vascular plant species of the European flora have been used as the basis for our analysis. The complete list of 3,143 taxa has been used as the reference for the Swiss flora. The distributions of the species are illustrated in coincidence maps based on the computer database of the Data Centre of the Swiss Flora in Geneva, Switzerland. Our study demonstrates clearly that the Atlantic flora of Europe requires a new biogeographical appraisal. The Swiss flora comprises 66 Atlantic and Mediterranean–Atlantic taxa, which are taxonomically and ecologically highly diverse. Switzerland contains 44% of all European Sub-Atlantic plants. This confirms the Sub-Atlantic geographical position of Switzerland. Only one Eu-Atlantic species growing in Switzerland, Vicia orobus, can be classified as native with certainty. This species is critically endangered and merits the highest conservation priority. Although a very alpine country, Switzerland has a relatively large number of Mediterranean–Atlantic species. The Atlantic and Mediterranean–Atlantic plants are a very threatened group in Switzerland, with wetland plants the most imperilled ecological group. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Database on Demand – An online tool for the custom generation of FASTA‐formatted sequence databases

In mass spectrometry‐based proteomics, most conventional search engines match spectral data to sequence databases. These search databases thus play a crucial role in the identification process. While search engines can derive peptides in silico from protein sequences, this is usually limited to standard digestion algorithms. Customized search databases that provide detailed control over the search space can vastly outperform such standard strategies, especially in gel‐free proteomics experiments. Here we present Database on Demand, an easy‐to‐use web tool that can quickly produce a wide variety of customized search databases.