Informing and influencing the interface between biodiversity science and biodiversity policy in South Africa

South Africa, as a megadiverse country (±21 700 vascular plants, 4800 vertebrates and 68 900 invertebrates described), is presently engaged with an extended, modified Global Strategy for Plant Conservation (GSPC). The country is fortunate in having a strong tradition of systematics research and, inter alia, houses several million preserved plant specimens (±1 million databased and georeferenced), allowing taxonomists and conservationists to track both the occurrence and distribution of indigenous and naturalized plant species. These rich local resources have been extensively drawn upon to deliver, with varying degrees of success, the 16 outcome-oriented GSPC 2010 Targets. The National Environmental Management: Biodiversity Act (NEMBA, 2004), the National Biodiversity Strategy and Action Plan (NBSAP) and the National Biodiversity Framework (NBF) have provided a robust legislative, enabling and policy framework for making operational and advancing GSPC-related efforts. However, within an emerging economy, the conservation of biodiversity has competed for government resources with housing, sanitation, primary education, basic health care and crime prevention, delivery of which translates to the currency of politicians: votes. A key challenge identified by local (and global) biodiversity scientists for the current GSPC phase is broad-scale advocacy, communicating the changing state of nature, and the inter-relatedness of biodiversity and human well-being. The nature of meeting this challenge is explored.     

Towards a coherent nomenclature of plant viruses

正The International Committee on Taxonomy of Viruses(ICTV)has the decree to set the rules for the classification and naming of viruses.The species is the lowest level considered in the taxonomic hierarchy.In general,virus species are named according to the structure"isolation hostsymptomsand the word‘virus’".A typical example is Tobacco mosaic virus[Genus:To-     

Towards a multisensor station for automated biodiversity monitoring

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas.To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution.     

Towards indicators of butterfly biodiversity based on a multiscale landscape description

The conservation of biodiversity has gained prominence in ecological research for the last decades. Conservation actions require a measure of biodiversity such as species richness, but its assessment is very difficult, even for small areas and therefore the search for surrogates (i.e. indicators) of biodiversity has emerged as an active research topic. We investigated the relationships between butterfly species richness and landscape structure and composition in two pine plantation sites in Southwest France. We assessed the correlation between butterfly species richness and a set of 15 landscape metrics computed for 18 land-uses at 10 different spatial scales. Spatial scales were accounted for by computing landscape metrics for circular buffers with radius ranging from 100 to 1000 m. The joint use of the Partial Least Squares Regression (PLSR) and a stepwise regression procedure revealed strong correlations between butterfly species richness and various landscape metrics in both study sites. The selected landscape metrics differed from one site to another and mostly involved measures of landscape fragmentation. We found a very strong effect of the spatial scale of investigation upon the perception of the landscape–butterfly richness relationship. Our main conclusions are that (i) certain landscape attributes can potentially serve as indicators for butterfly species richness at the landscape scale; (ii) future indicators of biodiversity based on landscape features should consider various spatial scales.     

Towards a science of informed matter

Over the last couple of decades, a call has begun to resound in a number of distinct fields of inquiry for a reattachment of form to matter, for an understanding of 'information' as inherently embodied, or, as Jean-Marie Lehn calls it, for a "science of informed matter." We hear this call most clearly in chemistry, in cognitive science, in molecular computation, and in robotics-all fields looking to biological processes to ground a new epistemology. The departure from the values of a more traditional epistemological culture can be seen most clearly in changing representations of biological development. Where for many years now, biological discourse has accepted a sharp distinction (borrowed directly from classical computer science) between information and matter, software and hardware, data and program, encoding and enactment, a new discourse has now begun to emerge in which these distinctions have little meaning. Perhaps ironically, much of this shift depends on drawing inspiration from just those biological processes which the discourse of disembodied information was intended to describe.     

Towards a collaborative, global infrastructure for biodiversity assessment

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.     

South Africa--serious about biodiversity science

A new government act, the creation of several centres of excellence and an injection of funding all indicate that biodiversity science is thriving in South Africa.     

Towards recommending visualizations for biodiversity data

To address the critical challenges of biodiversity conservation and study its impact on the ecosystem, over the last decade, scientists have been producing a large amount of highly heterogeneous and distributed data. For managing, processing, and visualizing this data, requires informatics skills. While many biologists lack these skills, informaticians are limited in their understanding of biological domain requirements and the context of the data. The focus of our research study is to assist scientists with the suggestion of possible visualizations for exploring and understanding their data. To be useful, such suggestions need to be based on the visualization knowledge of domain experts. We intend to gather such knowledge and use in the development of a visualization recommendation framework serving the biodiversity research community. Therefore, the authors want to encourage readers to share their domain knowledge on the biodiversity data visualization usage by participating in an online survey.     

Towards the construction of high-quality mutagenesis libraries

Objectives

To improve the quality of mutagenesis libraries in directed evolution strategy.

Results

In the process of library transformation, transformants which have been shown to take up more than one plasmid might constitute more than 20% of the constructed library, thereby extensively impairing the quality of the library. We propose a practical transformation method to prevent the occurrence of multiple-plasmid transformants while maintaining high transformation efficiency. A visual library model containing plasmids expressing different fluorescent proteins was used. Multiple-plasmid transformants can be reduced through optimizing plasmid DNA amount used for transformation based on the positive correlation between the occurrence frequency of multiple-plasmid transformants and the logarithmic ratio of plasmid molecules to competent cells.

Conclusions

This method provides a simple solution for a seemingly common but often neglected problem, and should be valuable for improving the quality of mutagenesis libraries to enhance the efficiency of directed evolution strategies.

     

Towards a taxonomically unbiased European Union biodiversity strategy for 2030

Through the Habitats Directive (92/43/EEC) and the financial investments of the LIFE projects, Europe has become an experimental arena for biological conservation. With an estimated annual budget of €20 billion, the EU Biodiversity Strategy for 2030 has set an ambitious goal of classifying 30% of its land and sea territory as Protected Areas and ensuring no deterioration in conservation trends and the status of protected species. We analysed LIFE projects focused on animals from 1992 to 2018 and found that investment in vertebrates was six times higher than that for invertebrates (€970 versus €150 million), with birds and mammals alone accounting for 72% of species and 75% of the total budget. In relative terms, investment per species towards vertebrates has been 468 times higher than that for invertebrates. Using a trait-based approach, we show that conservation effort is primarily explained by species'' popularity rather than extinction risk or body size. Therefore, we propose a roadmap to achieve unbiased conservation targets for 2030 and beyond.     

Evolution of interdisciplinarity in biodiversity science

The study of biodiversity has grown exponentially in the last thirty years in response to demands for greater understanding of the function and importance of Earth's biodiversity and finding solutions to conserve it. Here, we test the hypothesis that biodiversity science has become more interdisciplinary over time. To do so, we analyze 97,945 peer‐reviewed articles over a twenty‐two‐year time period (1990–2012) with a continuous time dynamic model, which classifies articles into concepts (i.e., topics and ideas) based on word co‐occurrences. Using the model output, we then quantify different aspects of interdisciplinarity: concept diversity, that is, the diversity of topics and ideas across subdisciplines in biodiversity science, subdiscipline diversity, that is, the diversity of subdisciplines across concepts, and network structure, which captures interactions between concepts and subdisciplines. We found that, on average, concept and subdiscipline diversity in biodiversity science were either stable or declining, patterns which were driven by the persistence of rare concepts and subdisciplines and a decline in the diversity of common concepts and subdisciplines, respectively. Moreover, our results provide evidence that conceptual homogenization, that is, decreases in temporal β concept diversity, underlies the observed trends in interdisciplinarity. Together, our results reveal that biodiversity science is undergoing a dynamic phase as a scientific discipline that is consolidating around a core set of concepts. Our results suggest that progress toward addressing the biodiversity crisis via greater interdisciplinarity during the study period may have been slowed by extrinsic factors, such as the failure to invest in research spanning across concepts and disciplines. However, recent initiatives such as the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services (IPBES) may attract broader support for biodiversity‐related issues and hence interdisciplinary approaches to address scientific, political, and societal challenges in the coming years.     

Trends in Romanian biodiversity conservation policy

Romania's commitment and ability to protect its environment inthe long term is challenged by several problems: insufficient financialmechanisms, monitoring, enforcement, and the information dissemination capacityof local environment protection agencies. History indicates that periods ofeconomic and social transition are very dangerous to biodiversity conservation.The demonstrated tendency during such periods gives priority to short-termincome-generating activities. Romanian conservation policy has had to adapt tothis change of circumstances. New sites have been included in the nationalprotected system and new legislation has been developed. But is this enough? Dothese satisfy progressive concepts and IUCN recommendations? This paper isintended to make recommendations, based on intersectoral participatoryplanning, for nature resources management. It focuses on how biodiversityconservation is being encouraged and developed at a national level.     

Towards the global monitoring of biodiversity change

Governments have set the ambitious target of reducing biodiversity loss by the year 2010. The scientific community now faces the challenge of assessing the progress made towards this target and beyond. Here, we review current monitoring efforts and propose a global biodiversity monitoring network to complement and enhance these efforts. The network would develop a global sampling programme for indicator taxa (we suggest birds and vascular plants) and would integrate regional sampling programmes for taxa that are locally relevant to the monitoring of biodiversity change. The network would also promote the development of comparable maps of global land cover at regular time intervals. The extent and condition of specific habitat types, such as wetlands and coral reefs, would be monitored based on regional programmes. The data would then be integrated with other environmental and socioeconomic indicators to design responses to reduce biodiversity loss.     

Towards next-generation biodiversity assessment using DNA metabarcoding

Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA (soil, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next-generation sequencing platforms and the ecologists' need for high-throughput taxon identification have facilitated the emergence of DNA metabarcoding. The potential power of DNA metabarcoding as it is implemented today is limited mainly by its dependency on PCR and by the considerable investment needed to build comprehensive taxonomic reference libraries. Further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries composed of whole organellar genomes and repetitive ribosomal nuclear DNA can be built based on the well-curated DNA extract collections maintained by standardized barcoding initiatives. The near-term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research.