Gregor Hagedorn

Description of Colletotrichum lupini comb. nov. in modern terms

Gloeosporium lupini Bondar is transferred to Colletotrichum. The fungus is characterized morphologically and illustrated. The two varieties, Colletotrichum lupini (Bondar) Nirenberg, Feiler & Hagedorn, comb. nov. var. lupini and Colletotrichum lupini var. setosum Nirenberg, Feiler & Hagedorn var. nov. are described. They are compared with additional Colletotrichum species reported from lupins and other hosts by morphological and physiological methods as well as by RAPD-PCR and DNA-sequencing.

Fauna Europaea – all European animal species on the web

Abstract Fauna Europaea is Europes main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information

Abstract The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.

A COMPREHENSIVE REFERENCE MODEL FOR BIOLOGICAL COLLECTIONS AND SURVEYS

The article describes an extended entity-relationship model covering biological collections, i.e. natural history collections of biotic origin; data collections used in floristic or faunistic mapping, survey, and monitoring projects; live collections such as botanical or zoological gardens, seed banks, microbial strain collections and gene banks; as well as novel collection kinds such as of secondary metabolites or DNA samples. The central element in the model is the unit, which stands for any object containing, being or being part of a living, fossilised, or conserved organism. The unit may be gathered (observed or collected) in the field and derived units may recursively emerge from it through specimen processing, breeding or cultivation. In addition, units may form associations (e.g. host/parasite), ensembles (lichen on a rock with fossils), and assemblages (herd, artificial grouping). Gathering events, specimen management (acquisition, accession, storage, preservation, exchange, ownership), and taxonomic or other identifications relate to the unit and are treated in detail. Geographic and geo-ecological data have not been fully modelled; taxonomic (name) data and descriptive information are treated by reference to other published models.

Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID

Abstract Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.

The genus Laetiporus (Basidiomycota, Polyporales) in East Asia.

Relationships among East Asian, North American and European Laetiporus sulphureus s. lat., a cosmopolitan brown rot species complex, were assessed with phylogenetic analyses and incompatibility tests. Three East Asian taxa, Laetiporus cremeiporus sp. nov., Laetiporus montanus and Laetiporus versisporus, are described and illustrated as well as compared with related taxa from Southeast Asia, North America and Europe. Phylogenetic analyses showed that L. cremeiporus and L. versisporus are clearly distinct species among Laetiporus taxa. The three conifer inhabiting species, Laetiporus conifericola, Laetiporus huroniensis and L. montanus, are closely related to each other. The European population of L. montanus exhibits two sequence variants of the EF1alpha: one is the same as observed in L. sulphureus in Europe and the other is that observed in East Asian population of L. montanus. A key to the known species of Laetiporus in the northern hemisphere is provided.

Scientific names of organisms: attribution, rights, and licensing

BackgroundAs biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world.FindingsThe laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts.ConclusionsA ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.

Community next steps for making globally unique identifiers work for biocollections data

Abstract Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

Abstract Background. The 7th Framework Programme for Research and Technological Development is helping the European Union to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights. We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information. Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.

Taxonomy and phylogeny of Puccinia lagenophorae: a study using rDNA sequence data, morphological and host range features

Puccinia lagenophorae is a rust fungus originating from Australasia which has spread throughout the world. A phylogenetic analysis of taxa related to this species was performed using rDNA (LSU, ITS) sequence data. The analyses revealed a well-supported cluster including all specimens of P. lagenophorae. By evaluating morphological and sequence data, the species is taxonomically re-defined and a list of synonyms is provided. Puccinia distincta on Bellis perennis, a species recently separated from P. lagenophorae, P. saccardoi, a species on the Goodeniaceae, and P. byliana, a species so far only known from South Africa, are reduced to synonymy in P. lagenophorae, as are several other species. Our analysis indicates that P. lagenophorae is likely not derived from the northern hemisphere species P. obscura, but from a species from Australia host-alternating between Asteraceae (aecial host) and Cyperaceae/Juncaceae (telial host). Another related species, P. stylidii (on Stylidium sp., Stylidiaceae) may have been derived from the same parental species as P. lagenophorae. From ontogenetical and morphological studies, the presence of pycnia could not be confirmed in the life cycle of this species, and the width of the pedicel of teliospores at the point of attachment was found to be highly variable and not a taxonomic character. The number of known host species is approximately 150, including 41 new host plants recorded herein.