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List of groups and committees that oversee the day to day operation of the European Genomic Data Infrasatructure

Phylogenetic relationships in Inuleae subtribe Inulinae (Asteraceae) were investigated. DNA sequence data from three chloroplast regions (ndhF, trnL-F and psbA-trnH) and the nuclear ribosomal internal transcribed spacer (ITS) region were analysed separately and in combination using parsimony and Bayesian inference. A total of 163 ingroup taxa were included, of which 60 were sampled for all four markers. Conflicts between chloroplast and nuclear data were assessed using partitioned Bremer support (PBS). Rather than averaging PBS over several trees from constrained searches, individual trees were considered by evaluating PBS ranges. Criteria to be used in the detection of a significant conflict between data partitions are proposed. Three nodes in the total data tree were found to encompass significant conflict that could result from ancient hybridization. Neither of the large, heterogeneous and widespread genera Inula and Pulicaria is monophyletic. A monophyletic group ("the Inula complex") that comprises all species of Inula includes also Telekia, Carpesium, Chrysophthalmum, Rhanteriopsis, Amblyocarpum, and Pentanema sensu stricto. Two species of Pentanema were found to be closer to Blumea (including Blumeopsis and Merrittia) and Caesulia. The monophyletic "Pulicaria complex" includes all taxa with heteromorphic pappus. Within this group, Francoeuria is distinct from Pulicaria and merits recognition as a separate genus. © The Willi Hennig Society 2009.

Athroismeae is a small tribe of the Asteraceae-Asteroideae, the members of which show considerable variation in morphology. A molecular phylogenetic study of the tribe is presented for the first ti ...

The DINA Symposium (“DIgital information system for NAtural history data”, https://dina-project.net) ends with a plenary session involving the audience to discuss the interplay of collection management and software tools. The discussion will touch different areas and issues such as: (1) Collection management using modern technology: How should and could collections be managed using current technology – What is the ultimate objective of using a new collection management system? How should traditional management processes be changed? (2) Development and community Why are there so many collection management systems? Why is it so difficult to create one system that fits everyone’s requirements? How could the community of developers and collection staff be built around DINA project in the future? (3) Features and tools How to identify needs that are common to all collections? What are the new tools and technologies that could facilitate collection management? How could those tools be implemented as DINA compliant services? (4) Data What data must be captured about collections and specimens? What criteria need to be applied in order to distinguish essential and “nice-to-have” information? How should established data standards (e.g. Darwin Core & ABCD (Access to Biological Collection Data)) be used to share data from rich and diverse data models? In addition to the plenary discussion around these questions, we will agree on a streamlined format for continuing the discussion in order to write a white paper on these questions. The results and outcome of the session will constitute the basis of the paper and will be subsequently refined.

The DINA Consortium (“DIgital information system for NAtural history data”, https://dina-project.net, Fig. 1) was formed in order to provide a framework for like-minded large natural history collection-holding institutions to collaborate through a distributed Open Source development model to produce a flexible and sustainable collection management system. Target collections include zoological, botanical, mycological, geological and paleontological collections, living collections, biodiversity inventories, observation records, and molecular data. The DINA system is architected as a loosely-coupled set of several web-based modules. The conceptual basis for this modular ecosystem is a compilation of comprehensive guidelines for Web application programming interfaces (APIs) to guarantee the interoperability of its components. Thus, all DINA components can be modified or even replaced by other components without crashing the rest of the system as long as they are DINA compliant. Furthermore, the modularity enables the institutions to host only the components they need. DINA focuses on an Open Source software philosophy and on community-driven open development, so the contributors share their development resources and expertise outside of their own institutions. One of the overarching reasons to develop a new collection management system is the need to better model complex relationships between collection objects (typically specimens) involving their derivatives, preparations and storage. We will discuss enhancements made in the DINA data model to better represent these relationships and the influence it has on the management of these objects, and on the sharing of information. Technical detail of various components of the DINA system will be shown in other talks in this symposium followed by a discussion session.

In order to ensure long-term commitment to the DINA project (“DIgital information system for NAtural history data”, https://dina-project.net), it is essential to continuously deliver features of high value to the user community. This is also what agile software development methods try to achieve by emphasizing early delivery, rapid response to changes and close collaboration with users (see for example the Manifesto for Agile Software Development at http://agilemanifesto.org). We will give a brief overview on how current development of the DINA collection management system core is guided by agile principles. The mammal collection at the Swedish Museum of Natural History will be used as an example. Developing a cross-disciplinary collection management system is a complex task that poses many challenges: Which features should we focus on? What kinds of data should the system ultimately support? How can the system be flexible but still easy to use? Since we cannot do everything at once, we work towards a minimum viable product (MVP) that contains just enough features at a time to bring value for selected target users. In the mammal collection case, the MVP is the simplest product that is able to replace the functions of the current system used for managing the collection. As we begin to work with other collections, new MVPs are defined and used to guide further development. Thus, the set of features available will increase with each MVP, benefiting both new and current users. Another big challenge is migration of legacy data, which is labor intensive and involves standardizing data that are not compatible with the new system. To address these issues, we aim to build a flexible data model that allows less structured data to coexist with more complex, highly structured data. Migration should thus not require extensive data standardization, transformation and cleaning. The plan is to instead offer tools for transforming and cleaning the data after they have been imported. With the data in place, it will be easier for the user to provide feedback and suggest new features.

The DINA system (“DIgital information system for NAtural history data”, https://dina-project.net) consists of several web-based services that fulfill specific tasks. Most of the existing services are covering single core features in the collection management system and can be used either as integrated components in the DINA environment, or as stand-alone services. In this presentation single services will be highlighted as they represent technically interesting approaches and practical solutions for daily challenges in collection management, data curation and migration workflows. The focus will be on the following topics: (1) a generic reporting and label printing service, (2) practical decisions on taxonomic references in collection data and (3) the generic management and referencing of related research data and metadata: Reporting as presented in this context is defined as an extraction and subsequent compilation of information from the collection management system rather than just summarizing statistics. With this quite broad understanding of the term the DINA Reports & Labels Service (Museum für Naturkunde Berlin 2018) can assist in several different collection workflows such as generating labels, barcodes, specimen lists, vouchers, paper loan forms etc. As it is based on customizable HTML templates, it can be even used for creating customized web forms for any kind of interaction (e.g. annotations). Many collection management systems try to cope with taxonomic issues, because in practice taxonomy is used not only for determinations, but also for organizing the collections and categorizing storage units (e.g. “Coleoptera hall”). Addressing taxonomic challenges in a collection management system can slow down development and add complexity for the users. The DINA system uncouples these issues in a simple taxonomic service for the sole assignment of names to specimens, for example determinations. This draws a clear line between collection management and taxonomic research, of which the latter can be supported in a separate service. While the digitization of collection data and workflows proceeds, linking related data is essential for data management and enrichment. In many institutions research data is disconnected from the collection specimen data because the type and structure cannot be easily included in the collection management databases. With the DINA Generic Data Module (Museum für Naturkunde Berlin 2017) a service exists that allows for attaching any relational data structures to the DINA system. It can also be used as a standalone service that accommodates structured data within a DINA compliant interface for data management.

The present study, based on sequences of cpDNA (trnL-F & psbA-trnH) and nrDNA (ITS) and morphology, examined the evolutionary relationships in Blumea and its position among related genera. The results confirmed that the closest relatives of Blumea are Caesulia, Duhaldea and Pentanema p.p., and showed that the monotypic genera Blumeopsis and Merrittia are nested within Blumea. In Blumea s.l., two major, well-supported clades were recognised and a single species, the widespread Blumea balsamifera, that could not be placed with certainty relative to the two main clades. The two main clades differ in habit, ecology and distribution. The Blumea densiflora clade contains shrubs and subshrubs of evergreen forests, distributed from continental Asia to New Guinea and Polynesia, whereas the Blumea lacera clade is a widespread paleotropical group that comprises mostly annual, weedy herbs of open forests and fields.

How does genome evolution affect the rate of diversification of biological lineages? Recent studies have suggested that the overall rate of genome evolution is correlated with the rate of diversification. If true, this claim has important consequences for understanding the process of diversification, and implications for the use of DNA sequence data to reconstruct evolutionary history. However, the generality and cause of this relationship have not been established. Here, we test the relationship between the rate of molecular evolution and net diversification with a 19-gene, 17-kb DNA sequence dataset from 64 families of birds. We show that rates of molecular evolution are positively correlated to net diversification in birds. Using a 7.6-kb dataset of protein-coding DNA, we show that the synonymous substitution rate, and therefore the mutation rate, is correlated to net diversification. Further analysis shows that the link between mutation rates and net diversification is unlikely to be the indirect result of correlations with life-history variables that may influence both quantities, suggesting that there might be a causal link between mutation rates and net diversification.

The phylogenetic relationships between the tribes Inuleae sensu stricto and Plucheeae are investigated by analysis of sequence data from the cpDNA gene ndhF. The delimitation between the two tribes is elucidated, and the systematic positions of a number of genera associated with these groups, i.e. genera with either aberrant morphological characters or a debated systematic position, are clarified. Together, the Inuleae and Plucheeae form a monophyletic group in which the majority of genera of Inuleae s.str. form one clade, and all the taxa from the Plucheeae together with the genera Antiphiona, Calostephane, Geigeria, Ondetia, Pechuel-loeschea, Pegolettia, and Iphionopsis from Inuleae s.str. form another. Members of the Plucheeae are nested with genera of the Inuleae s.str., and support for the Plucheeae clade is weak. Consequently, the latter cannot be maintained and the two groups are treated as one tribe, Inuleae, with the two subtribes Inulinae and Plucheinae. The genera Asteriscus, Chrysophthalmum, Inula, Laggera, Pentanema, Pluchea, and Pulicaria are demonstrated to be non-monophyletic. Cratystylis and Iphionopsis are found to belong to the same clade as the taxa of the former Plucheeae. Caesulia is shown to be a close relative of Duhaldea and Blumea of the Inuleae-Inulinae. The genera Callilepis and Zoutpansbergia belong to the major clade of the family that includes the tribes Heliantheae sensu lato and Inuleae (incl. Plucheeae), but their exact position remains unresolved. The genus Gymnarrhena is not part of the Inuleae, but is either part of the unresolved basal complex of the paraphyletic Cichorioideae, or sister to the entire Asteroideae.